From 974c89da6ad5c59740f29a1ff8f0148cd4a21207 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:30:42 -0400 Subject: [PATCH 001/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..69312e8fc --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = e10cbf6c-d927-464c-8bba-bb4fde8554da diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..3ead620e3 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 3ead620e3154a7bf1193b73e4d5fcb9043d4b98a From 5d2e100a78861b5f525e8ffef2e2fdceac3db5c5 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:31:44 -0400 Subject: [PATCH 002/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-001_acq-axial_localizer.json | 81 +++ .../sub-01_ses-001_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-001_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-001_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-001_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-001_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-001/anat/sub-01_ses-001_scout.json | 542 ++++++++++++++++++ .../ses-001/anat/sub-01_ses-001_scout.nii.gz | 1 + ...1_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ...-001_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-01_part-mag_events.tsv | 1 + ...001_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-01_part-phase_events.tsv | 1 + ...1_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-001_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-02_part-mag_events.tsv | 1 + ...001_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-02_part-phase_events.tsv | 1 + ...1_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + sub-01/ses-001/sub-01_ses-001_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 51 files changed, 3485 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-001/anat/sub-01_ses-001_acq-axial_localizer.json create mode 120000 sub-01/ses-001/anat/sub-01_ses-001_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_localizer.json create mode 120000 sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-001/anat/sub-01_ses-001_acq-sagittal_localizer.json create mode 120000 sub-01/ses-001/anat/sub-01_ses-001_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-001/anat/sub-01_ses-001_scout.json create mode 120000 sub-01/ses-001/anat/sub-01_ses-001_scout.nii.gz create mode 100644 sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_part-phase_sbref.nii.gz create mode 120000 sub-01/ses-001/sub-01_ses-001_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 3ead620e3..f6acb7e8d 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 3ead620e3154a7bf1193b73e4d5fcb9043d4b98a +Subproject commit f6acb7e8d6e81993fe054d36b3341a3a3a186a18 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-001/anat/sub-01_ses-001_acq-axial_localizer.json b/sub-01/ses-001/anat/sub-01_ses-001_acq-axial_localizer.json new file mode 100644 index 000000000..7c29ac6bf --- /dev/null +++ b/sub-01/ses-001/anat/sub-01_ses-001_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:40:24.035000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0417182, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 282.102 +} \ No newline at end of file diff --git a/sub-01/ses-001/anat/sub-01_ses-001_acq-axial_localizer.nii.gz b/sub-01/ses-001/anat/sub-01_ses-001_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..76a399416 --- /dev/null +++ b/sub-01/ses-001/anat/sub-01_ses-001_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/K5/f2/MD5E-s180441--7ce621b36f68c1c1ad8c0c7dccb55e2b.nii.gz/MD5E-s180441--7ce621b36f68c1c1ad8c0c7dccb55e2b.nii.gz \ No newline at end of file diff --git a/sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_localizer.json b/sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_localizer.json new file mode 100644 index 000000000..7f29e1c54 --- /dev/null +++ b/sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:40:31.025000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0417182, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 282.102 +} \ No newline at end of file diff --git a/sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_localizer.nii.gz b/sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_localizer.nii.gz new file mode 120000 index 000000000..a4d8ecefb --- /dev/null +++ b/sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/QX/q3/MD5E-s193713--65f08221d3b9fa6c417e07b87f90520a.nii.gz/MD5E-s193713--65f08221d3b9fa6c417e07b87f90520a.nii.gz \ No newline at end of file diff --git a/sub-01/ses-001/anat/sub-01_ses-001_acq-sagittal_localizer.json b/sub-01/ses-001/anat/sub-01_ses-001_acq-sagittal_localizer.json new file mode 100644 index 000000000..b8c1f29c8 --- /dev/null +++ b/sub-01/ses-001/anat/sub-01_ses-001_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:40:17.045000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 0, + 1, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Sag", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0417182, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SliceTiming": [ + 0, + 10.4844, + 3.49219 + ], + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 28, + "StationName": "MRC35049", + "TxRefAmp": 282.102 +} \ No newline at end of file diff --git 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newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..0e2764a76 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.992429, 0.117678, 0.0351625, -0.0992325, 0.936972, -0.335017], + 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"ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [629, -7189, -8820, 646, 101, -1, -51, 12], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 282.102, + "dcmmeta_affine": [ + [-1.9848581552505493, -0.1984649896621704, 0.14474104344844818, 111.55570220947266], + [-0.23535656929016113, 1.87394380569458, -0.6579830646514893, -48.20921325683594], + [0.07032499462366104, 0.6700343489646912, 1.8831113576889038, -60.89922332763672], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 45750fa7febad4772c4d14c445e3639b76d1ad4b Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:33:25 -0400 Subject: [PATCH 003/463] fix fmap phase --- ...1_ses-001_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-001_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-001_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - sub-01/ses-001/sub-01_ses-001_scans.tsv | 2 +- 17 files changed, 1 insertion(+), 638 deletions(-) rename sub-01/ses-001/fmap/{sub-01_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-001_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-001/fmap/{sub-01_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-001_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-001/fmap/{sub-01_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-001_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-001/fmap/{sub-01_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-001_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-001/fmap/{sub-01_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-001_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-001/fmap/{sub-01_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-001_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-001/fmap/{sub-01_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-001_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-001/fmap/{sub-01_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-001_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 96fc334f3..000000000 --- a/sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:41:24.887500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.992429, 0.117678, 0.0351625, -0.0992325, 0.936972, -0.335017], - "ImageOrientationText": "Tra>Cor(-19.3)>Sag(4.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.049004, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [629, -7189, -8820, 646, 101, -1, -51, 12], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 282.102, - "WipMemBlock": "7c55f30a-db3f-4dd6-894c-f74be3574499||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9848581552505493, -0.1984649896621704, 0.14474104344844818, 111.55570220947266], - [-0.23535656929016113, 1.87394380569458, -0.6579830646514893, -48.20921325683594], - [0.07032499462366104, 0.6700343489646912, 1.8831113576889038, -60.89922332763672], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99242905053973, 0.1176782838234, 0.03516249651528, -0.0992324922002, 0.93697192971058, -0.3350171867624], - "ImagePositionPatient": [-741.36090055978, -912.59236022863, 226.40853229352], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.25882, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "113918.303000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.04900398832809, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "114211.482000", - "SliceLocation": -33.406242085765, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999542604, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "113918.213000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["114124.887500", "114126.377500", "114127.867500"], - "ContentTime": ["114211.485000", "114211.487000", "114211.490000"], - "InstanceCreationTime": ["114211.485000", "114211.487000", "114211.490000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4828.0, 4808.0, 4804.0], - "WindowWidth": [18634.0, 18604.0, 18604.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index e68bbf26e..000000000 --- a/sub-01/ses-001/fmap/sub-01_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/kM/8v/MD5E-s3335516--d883d63afd518faf86ed270424600aba.nii.gz/MD5E-s3335516--d883d63afd518faf86ed270424600aba.nii.gz \ No newline at end of file diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 0d099cb65..000000000 --- a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:41:14.457500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992429, - 0.117678, - 0.0351625, - -0.0992325, - 0.936972, - -0.335017 - ], - "ImageOrientationText": "Tra>Cor(-19.3)>Sag(4.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.049004, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 629, - -7189, - -8820, - 646, - 101, - -1, - -51, - 12 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 282.102, - "WipMemBlock": "7c55f30a-db3f-4dd6-894c-f74be3574499||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index c73caa070..000000000 --- a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/8q/WG/MD5E-s1112335--77b3bbc039fb4f0b570ba58cc8df7f93.nii.gz/MD5E-s1112335--77b3bbc039fb4f0b570ba58cc8df7f93.nii.gz \ No newline at end of file diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 7220a4775..000000000 --- a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:42:59.745000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992429, - 0.117678, - 0.0351625, - -0.0992325, - 0.936972, - -0.335017 - ], - "ImageOrientationText": "Tra>Cor(-19.3)>Sag(4.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0614467, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 629, - -7189, - -8820, - 646, - 101, - -1, - -51, - 12 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 282.102, - "WipMemBlock": "ca2d2a2a-b5fe-4f02-a07e-c4130739f328||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 68476d172..000000000 --- a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/vw/2J/MD5E-s1103604--8a5a0cd34a54cea8d255cd7031e983dc.nii.gz/MD5E-s1103604--8a5a0cd34a54cea8d255cd7031e983dc.nii.gz \ No newline at end of file diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index ddda195cc..000000000 --- a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:52:55.327500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992429, - 0.117678, - 0.0351625, - -0.0992325, - 0.936972, - -0.335017 - ], - "ImageOrientationText": "Tra>Cor(-19.3)>Sag(4.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0614467, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 629, - -7189, - -8820, - 646, - 101, - -1, - -51, - 12 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 282.102, - "WipMemBlock": "1616fbf7-e063-4743-b23e-409d0113c5bd||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index c6614ad89..000000000 --- a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/p7/0J/MD5E-s1103893--d2f65ac581561873eac6aa418dd2da04.nii.gz/MD5E-s1103893--d2f65ac581561873eac6aa418dd2da04.nii.gz \ No newline at end of file diff --git a/sub-01/ses-001/sub-01_ses-001_scans.tsv b/sub-01/ses-001/sub-01_ses-001_scans.tsv index 58e40614a..c9eb589e1 120000 --- a/sub-01/ses-001/sub-01_ses-001_scans.tsv +++ b/sub-01/ses-001/sub-01_ses-001_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/3F/ww/MD5E-s2045--3ba6fa3d897e193f2cf78173e28795f6.tsv/MD5E-s2045--3ba6fa3d897e193f2cf78173e28795f6.tsv \ No newline at end of file +../../.git/annex/objects/FF/7P/MD5E-s1565--0425ca25b7a01af8d70d4fa8b1e8e727.tsv/MD5E-s1565--0425ca25b7a01af8d70d4fa8b1e8e727.tsv \ No newline at end of file From 17b8bb475eeb0aec000b442e0a896d8d18c4f8d6 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:33:56 -0400 Subject: [PATCH 004/463] fix complex event files --- ...g_events.tsv => sub-01_ses-001_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-001_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-001_task-mario3_run-02_part-mag_events.tsv | 1 - .../func/sub-01_ses-001_task-mario3_run-02_part-phase_events.tsv | 1 - 4 files changed, 2 deletions(-) rename sub-01/ses-001/func/{sub-01_ses-001_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-001_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-001/func/{sub-01_ses-001_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-001_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_part-mag_events.tsv delete mode 120000 sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_part-phase_events.tsv diff --git a/sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-001/func/sub-01_ses-001_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 0e82725a56828bd59bd91dffdf88adc5de66d152 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:34:42 -0400 Subject: [PATCH 005/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..4d851a497 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = f77115e0-6293-4cb6-95ea-6d7a4b5d703b diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..0fcfac4c4 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 0fcfac4c4032c888c78583c70fbf92e614c8f0eb From 124171508a3932e1e125cccbf0bea2e81036ef57 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:34:58 -0400 Subject: [PATCH 006/463] fill IntendedFor --- ...1_ses-001_acq-sbref_dir-AP_run-01_epi.json | 89 ++----------------- ...1_ses-001_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-001_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- 3 files changed, 22 insertions(+), 243 deletions(-) diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_epi.json index 5a80fcff4..321b587d2 100644 --- a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992429, - 0.117678, - 0.0351625, - -0.0992325, - 0.936972, - -0.335017 - ], + "ImageOrientationPatientDICOM": [0.992429, 0.117678, 0.0351625, -0.0992325, 0.936972, -0.335017], "ImageOrientationText": "Tra>Cor(-19.3)>Sag(4.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,16 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-01_ses-001_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-001/func/sub-01_ses-001_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +64,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 629, - -7189, - -8820, - 646, - 101, - -1, - -51, - 12 - ], + "ShimSetting": [629, -7189, -8820, 646, 101, -1, -51, 12], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_epi.json index c46c07cff..f78ee65ec 100644 --- a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992429, - 0.117678, - 0.0351625, - -0.0992325, - 0.936972, - -0.335017 - ], + "ImageOrientationPatientDICOM": [0.992429, 0.117678, 0.0351625, -0.0992325, 0.936972, -0.335017], "ImageOrientationText": "Tra>Cor(-19.3)>Sag(4.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-01_ses-001_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 629, - -7189, - -8820, - 646, - 101, - -1, - -51, - 12 - ], + "ShimSetting": [629, -7189, -8820, 646, 101, -1, -51, 12], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_epi.json index 1e21728c7..fa5151dc6 100644 --- a/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992429, - 0.117678, - 0.0351625, - -0.0992325, - 0.936972, - -0.335017 - ], + "ImageOrientationPatientDICOM": [0.992429, 0.117678, 0.0351625, -0.0992325, 0.936972, -0.335017], "ImageOrientationText": "Tra>Cor(-19.3)>Sag(4.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-01_ses-001_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 629, - -7189, - -8820, - 646, - 101, - -1, - -51, - 12 - ], + "ShimSetting": [629, -7189, -8820, 646, 101, -1, -51, 12], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From c24970a710b6f90c270bd901107bc68d39288011 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:35:38 -0400 Subject: [PATCH 007/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-009_acq-axial_localizer.json | 81 +++ .../sub-01_ses-009_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-009_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-009_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-009_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-009_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-009/anat/sub-01_ses-009_scout.json | 542 ++++++++++++++++++ .../ses-009/anat/sub-01_ses-009_scout.nii.gz | 1 + ...9_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ...-009_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...09_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...009_task-mario3_run-01_part-mag_events.tsv | 1 + ...009_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...09_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-01_part-phase_events.tsv | 1 + ...9_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + sub-01/ses-009/sub-01_ses-009_scans.tsv | 1 + task-mario3_bold.json | 81 +++ 37 files changed, 2529 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-009/anat/sub-01_ses-009_acq-axial_localizer.json create mode 120000 sub-01/ses-009/anat/sub-01_ses-009_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-009/anat/sub-01_ses-009_acq-coronal_localizer.json create mode 120000 sub-01/ses-009/anat/sub-01_ses-009_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-009/anat/sub-01_ses-009_acq-sagittal_localizer.json create mode 120000 sub-01/ses-009/anat/sub-01_ses-009_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-009/anat/sub-01_ses-009_scout.json create mode 120000 sub-01/ses-009/anat/sub-01_ses-009_scout.nii.gz create mode 100644 sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_part-phase_sbref.nii.gz create mode 120000 sub-01/ses-009/sub-01_ses-009_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 0fcfac4c4..2557d35b7 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 0fcfac4c4032c888c78583c70fbf92e614c8f0eb +Subproject commit 2557d35b7d8fa537485e6d782ee0ee16a48b8eb8 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-009/anat/sub-01_ses-009_acq-axial_localizer.json b/sub-01/ses-009/anat/sub-01_ses-009_acq-axial_localizer.json new file mode 100644 index 000000000..4760eee5a --- /dev/null +++ b/sub-01/ses-009/anat/sub-01_ses-009_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:24:27.047500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": 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"PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0551811, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 316.832 +} \ No newline at end of file diff --git a/sub-01/ses-009/anat/sub-01_ses-009_acq-axial_localizer.nii.gz b/sub-01/ses-009/anat/sub-01_ses-009_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..5aca27af0 --- /dev/null +++ b/sub-01/ses-009/anat/sub-01_ses-009_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ 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[-1.986812710762024, -0.17522145807743073, 0.14789408445358276, 110.50180053710938], + [-0.21853496134281158, 1.8375500440597534, -0.7587175965309143, -45.71659469604492], + [0.06940958648920059, 0.7698748707771301, 1.8445799350738525, -73.29668426513672], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_shape": [104, 104, 60, 365], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 9d031daf559996b2036eef73c583400c85761ad5 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:37:05 -0400 Subject: [PATCH 008/463] fix fmap phase --- ...1_ses-009_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-009_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-009_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-009_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - sub-01/ses-009/sub-01_ses-009_scans.tsv | 2 +- 13 files changed, 1 insertion(+), 485 deletions(-) rename sub-01/ses-009/fmap/{sub-01_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-009_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-009/fmap/{sub-01_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-009_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-009/fmap/{sub-01_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-009_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-009/fmap/{sub-01_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-009_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-009/fmap/{sub-01_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-009_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-009/fmap/{sub-01_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-009_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz diff --git a/sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 0cc8101f0..000000000 --- a/sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:25:28.615000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.993406, 0.109267, 0.0347048, -0.0876107, 0.918775, -0.384937], - "ImageOrientationText": "Tra>Cor(-22.4)>Sag(4.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - 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0.14789408445358276, 110.50180053710938], - [-0.21853496134281158, 1.8375500440597534, -0.7587175965309143, -45.71659469604492], - [0.06940958648920059, 0.7698748707771301, 1.8445799350738525, -73.29668426513672], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99340635970004, 0.10926747794133, 0.03470479465238, -0.0876107273012, 0.9187750138746, -0.3849374421143], - "ImagePositionPatient": [-751.87321296576, -891.96599293084, 260.96979750579], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.258856, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "112338.114000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.06481814639028, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "112614.549000", - "SliceLocation": -42.086520478297, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000118305, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "112338.014000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["112528.615000", "112530.105000", "112531.595000"], - "ContentTime": ["112614.551000", "112614.553000", "112614.556000"], - "InstanceCreationTime": ["112614.551000", "112614.553000", "112614.556000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4812.0, 4784.0, 4814.0], - "WindowWidth": [18610.0, 18576.0, 18608.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index ad5e5c86c..000000000 --- a/sub-01/ses-009/fmap/sub-01_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/z0/Qf/MD5E-s3335175--8c306065707fa4aa14bb9b1db965182c.nii.gz/MD5E-s3335175--8c306065707fa4aa14bb9b1db965182c.nii.gz \ No newline at end of file diff --git a/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 85a130969..000000000 --- a/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:25:18.185000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993406, - 0.109267, - 0.0347048, - -0.0876107, - 0.918775, - -0.384937 - ], - "ImageOrientationText": "Tra>Cor(-22.4)>Sag(4.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - 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- 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 316.832, - "WipMemBlock": "29a6195f-83fc-4d82-8905-7835ed6fddca||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index faa76d911..000000000 --- a/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/mV/j5/MD5E-s1112080--8fa392b19494a964171a2eb5b9622830.nii.gz/MD5E-s1112080--8fa392b19494a964171a2eb5b9622830.nii.gz \ No newline at end of file diff --git a/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 122119392..000000000 --- a/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:25:56.297500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993406, - 0.109267, - 0.0347048, - -0.0876107, - 0.918775, - -0.384937 - ], - "ImageOrientationText": "Tra>Cor(-22.4)>Sag(4.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0812763, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 636, - -7182, - -8844, - 614, - 101, - 24, - -98, - 16 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 316.832, - "WipMemBlock": "9aa88b81-38a8-45d3-bf49-626b0090722a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 12935adb8..000000000 --- a/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/41/71/MD5E-s1103867--be855fdd7bfc71174092d103dfdc1817.nii.gz/MD5E-s1103867--be855fdd7bfc71174092d103dfdc1817.nii.gz \ No newline at end of file diff --git a/sub-01/ses-009/sub-01_ses-009_scans.tsv b/sub-01/ses-009/sub-01_ses-009_scans.tsv index 1880430dd..d8e9131fb 120000 --- a/sub-01/ses-009/sub-01_ses-009_scans.tsv +++ b/sub-01/ses-009/sub-01_ses-009_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/09/2w/MD5E-s1423--11caa0359d543fb027202b3416cc2fb7.tsv/MD5E-s1423--11caa0359d543fb027202b3416cc2fb7.tsv \ No newline at end of file +../../.git/annex/objects/W8/91/MD5E-s1064--fc04706a0debc1d7f6066a25830d2971.tsv/MD5E-s1064--fc04706a0debc1d7f6066a25830d2971.tsv \ No newline at end of file From 349bbfc11efdb278b9f33c79eb0a1fc2acbc2bde Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:37:31 -0400 Subject: [PATCH 009/463] fix complex event files --- ...g_events.tsv => sub-01_ses-009_task-mario3_run-01_events.tsv} | 0 .../func/sub-01_ses-009_task-mario3_run-01_part-phase_events.tsv | 1 - 2 files changed, 1 deletion(-) rename sub-01/ses-009/func/{sub-01_ses-009_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-009_task-mario3_run-01_events.tsv} (100%) delete mode 120000 sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_part-phase_events.tsv diff --git a/sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From b3e8b0c618a972254d0dc020f69533ffe6bc16ec Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:37:33 -0400 Subject: [PATCH 010/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..ecd6ec3cb --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = e0e67be5-809d-4c82-aa45-a066c630f96a diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..e3b260c86 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit e3b260c867cfdd558660345799a5b71af8936b38 From 9af847044aadb97ad7fb3efe49d12b29d349b8ff Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:37:34 -0400 Subject: [PATCH 011/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..33d75b44f --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = f74e0525-c83d-402d-b965-7b4655516444 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..fa3d85441 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit fa3d85441cdadac349a49989868e10ed0907dc24 From a4e7205cd0940277e09eac27e2d744d88b4a09a2 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:38:05 -0400 Subject: [PATCH 012/463] fill IntendedFor --- ...1_ses-009_acq-sbref_dir-AP_run-01_epi.json | 88 ++----------------- ...1_ses-009_acq-sbref_dir-PA_run-01_epi.json | 88 ++----------------- 2 files changed, 14 insertions(+), 162 deletions(-) diff --git a/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_epi.json index bc8b76145..481745660 100644 --- a/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993406, - 0.109267, - 0.0347048, - -0.0876107, - 0.918775, - -0.384937 - ], + "ImageOrientationPatientDICOM": [0.993406, 0.109267, 0.0347048, -0.0876107, 0.918775, -0.384937], "ImageOrientationText": "Tra>Cor(-22.4)>Sag(4.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-009/func/sub-01_ses-009_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 636, - -7182, - -8844, - 614, - 101, - 24, - -98, - 16 - ], + "ShimSetting": [636, -7182, -8844, 614, 101, 24, -98, 16], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.02, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_epi.json index 9f9b6dd75..df834e145 100644 --- a/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-009/fmap/sub-01_ses-009_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993406, - 0.109267, - 0.0347048, - -0.0876107, - 0.918775, - -0.384937 - ], + "ImageOrientationPatientDICOM": [0.993406, 0.109267, 0.0347048, -0.0876107, 0.918775, -0.384937], "ImageOrientationText": "Tra>Cor(-22.4)>Sag(4.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-009/func/sub-01_ses-009_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 636, - -7182, - -8844, - 614, - 101, - 24, - -98, - 16 - ], + "ShimSetting": [636, -7182, -8844, 614, 101, 24, -98, 16], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 6dfda3cb87804cc1a83db6a24a4f21ec7f0ad22c Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:38:08 -0400 Subject: [PATCH 013/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..a06f32e7e --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = dcd570c0-e60a-49db-a6d6-358b5ef3022c diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..cb368e2f2 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit cb368e2f26cf75fb609054d15bcee5958f1eea03 From 6ead85132b45a750a7ba7f16c09dc2e19d7d7af5 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:38:14 -0400 Subject: [PATCH 014/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..6a2811a3c --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 40a183fd-8584-410f-9d44-0a128167c572 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..bbe7d7850 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit bbe7d7850d1825f4457f7c9ef101efdd983420f6 From 678885aba7cc1d784a7da124423f23f78f755fad Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:38:55 -0400 Subject: [PATCH 015/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-007_acq-axial_localizer.json | 81 +++ .../sub-01_ses-007_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-007_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-007_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-007_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-007_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-007/anat/sub-01_ses-007_scout.json | 542 ++++++++++++++++++ .../ses-007/anat/sub-01_ses-007_scout.nii.gz | 1 + ...7_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ...-007_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...07_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...007_task-mario3_run-01_part-mag_events.tsv | 1 + ...007_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...07_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-01_part-phase_events.tsv | 1 + ...7_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-007_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...07_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...007_task-mario3_run-02_part-mag_events.tsv | 1 + ...007_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...07_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-02_part-phase_events.tsv | 1 + ...7_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + sub-01/ses-007/sub-01_ses-007_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 51 files changed, 3485 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-007/anat/sub-01_ses-007_acq-axial_localizer.json create mode 120000 sub-01/ses-007/anat/sub-01_ses-007_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-007/anat/sub-01_ses-007_acq-coronal_localizer.json create mode 120000 sub-01/ses-007/anat/sub-01_ses-007_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-007/anat/sub-01_ses-007_acq-sagittal_localizer.json create mode 120000 sub-01/ses-007/anat/sub-01_ses-007_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-007/anat/sub-01_ses-007_scout.json create mode 120000 sub-01/ses-007/anat/sub-01_ses-007_scout.nii.gz create mode 100644 sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-phase_sbref.nii.gz create mode 120000 sub-01/ses-007/sub-01_ses-007_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index e3b260c86..f15b6ed33 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit e3b260c867cfdd558660345799a5b71af8936b38 +Subproject commit f15b6ed33cf84651dd051f65b17ecbc00cc811de diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-007/anat/sub-01_ses-007_acq-axial_localizer.json b/sub-01/ses-007/anat/sub-01_ses-007_acq-axial_localizer.json new file mode 100644 index 000000000..7c2fa8300 --- /dev/null +++ b/sub-01/ses-007/anat/sub-01_ses-007_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:39:46.035000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + 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"SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 294.962 +} \ No newline at end of file diff --git a/sub-01/ses-007/anat/sub-01_ses-007_acq-axial_localizer.nii.gz b/sub-01/ses-007/anat/sub-01_ses-007_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..856d88cae --- /dev/null +++ b/sub-01/ses-007/anat/sub-01_ses-007_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/kJ/g3/MD5E-s181892--3ae8523b999a7dd19d55ff07a29a86d4.nii.gz/MD5E-s181892--3ae8523b999a7dd19d55ff07a29a86d4.nii.gz \ No newline at end of file diff --git a/sub-01/ses-007/anat/sub-01_ses-007_acq-coronal_localizer.json b/sub-01/ses-007/anat/sub-01_ses-007_acq-coronal_localizer.json new file mode 100644 index 000000000..4668cf67f --- /dev/null +++ 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a/sub-01/ses-007/anat/sub-01_ses-007_acq-sagittal_localizer.nii.gz b/sub-01/ses-007/anat/sub-01_ses-007_acq-sagittal_localizer.nii.gz new file mode 120000 index 000000000..5bd8fb5af --- /dev/null +++ b/sub-01/ses-007/anat/sub-01_ses-007_acq-sagittal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/K6/Vf/MD5E-s632520--02bd9e994b1cbbc4bd49b7a0d2927056.nii.gz/MD5E-s632520--02bd9e994b1cbbc4bd49b7a0d2927056.nii.gz \ No newline at end of file diff --git a/sub-01/ses-007/anat/sub-01_ses-007_scout.json b/sub-01/ses-007/anat/sub-01_ses-007_scout.json new file mode 100644 index 000000000..24b40ec2b --- /dev/null +++ b/sub-01/ses-007/anat/sub-01_ses-007_scout.json @@ -0,0 +1,542 @@ +{ + "AcquisitionMatrixPE": 160, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:39:23.005000", + "BaseResolution": 160, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + 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b/sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-phase_sbref.nii.gz new file mode 120000 index 000000000..d8bb4340b --- /dev/null +++ b/sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Gx/F7/MD5E-s1103659--32961c13003dfa18128ed9228422f76e.nii.gz/MD5E-s1103659--32961c13003dfa18128ed9228422f76e.nii.gz \ No newline at end of file diff --git a/sub-01/ses-007/sub-01_ses-007_scans.tsv b/sub-01/ses-007/sub-01_ses-007_scans.tsv new file mode 120000 index 000000000..468cb4e8f --- /dev/null +++ b/sub-01/ses-007/sub-01_ses-007_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/G8/84/MD5E-s2045--41dc0da475790eccee63bb0d156dffa0.tsv/MD5E-s2045--41dc0da475790eccee63bb0d156dffa0.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..db4e426c4 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.993334, 0.114646, 0.0119647, -0.100374, 0.911342, -0.399225], + "ImageOrientationText": "Tra>Cor(-23.3)>Sag(3.2)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0647014, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [622, -7196, -8815, 629, 86, 26, -82, 9], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 294.962, + "dcmmeta_affine": [ + [-1.9866688251495361, -0.2007475197315216, 0.11334671080112457, 111.6868896484375], + [-0.2292911410331726, 1.8226839303970337, -0.7907267808914185, -44.587615966796875], + [0.02392939291894436, 0.798450767993927, 1.8335494995117188, -66.63365936279297], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From ea0cfdaa9f89bae608f271b76222a001d648b98f Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:38:56 -0400 Subject: [PATCH 016/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-016_acq-axial_localizer.json | 81 +++ .../sub-01_ses-016_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-016_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-016_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-016_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-016_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-016/anat/sub-01_ses-016_scout.json | 542 ++++++++++++++++++ .../ses-016/anat/sub-01_ses-016_scout.nii.gz | 1 + ...6_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-016_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...16_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...016_task-mario3_run-01_part-mag_events.tsv | 1 + ...016_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...16_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-01_part-phase_events.tsv | 1 + ...6_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-016_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...16_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...016_task-mario3_run-02_part-mag_events.tsv | 1 + ...016_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...16_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-02_part-phase_events.tsv | 1 + ...6_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-016_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...16_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...016_task-mario3_run-03_part-mag_events.tsv | 1 + ...016_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...16_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-03_part-phase_events.tsv | 1 + ...6_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-01/ses-016/sub-01_ses-016_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-016/anat/sub-01_ses-016_acq-axial_localizer.json create mode 120000 sub-01/ses-016/anat/sub-01_ses-016_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-016/anat/sub-01_ses-016_acq-coronal_localizer.json create mode 120000 sub-01/ses-016/anat/sub-01_ses-016_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-016/anat/sub-01_ses-016_acq-sagittal_localizer.json create mode 120000 sub-01/ses-016/anat/sub-01_ses-016_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-016/anat/sub-01_ses-016_scout.json create mode 120000 sub-01/ses-016/anat/sub-01_ses-016_scout.nii.gz create mode 100644 sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-01/ses-016/sub-01_ses-016_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index fa3d85441..53f5e4229 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit fa3d85441cdadac349a49989868e10ed0907dc24 +Subproject commit 53f5e4229fe5e2dff1b9972ee4d763a39e60385c diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-016/anat/sub-01_ses-016_acq-axial_localizer.json b/sub-01/ses-016/anat/sub-01_ses-016_acq-axial_localizer.json new file mode 100644 index 000000000..7aecc59c6 --- /dev/null +++ b/sub-01/ses-016/anat/sub-01_ses-016_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "17:13:38.065000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + 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\ No newline at end of file From dc6f1915550884af671e42d7e1232362f292eca5 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:39:25 -0400 Subject: [PATCH 017/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-014_acq-axial_localizer.json | 81 +++ .../sub-01_ses-014_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-014_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-014_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-014_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-014_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-014/anat/sub-01_ses-014_scout.json | 542 ++++++++++++++++++ .../ses-014/anat/sub-01_ses-014_scout.nii.gz | 1 + ...4_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-014_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...14_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...014_task-mario3_run-01_part-mag_events.tsv | 1 + ...014_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...14_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-01_part-phase_events.tsv | 1 + ...4_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-014_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...14_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...014_task-mario3_run-02_part-mag_events.tsv | 1 + ...014_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...14_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-02_part-phase_events.tsv | 1 + ...4_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-014_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...14_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...014_task-mario3_run-03_part-mag_events.tsv | 1 + ...014_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...14_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-03_part-phase_events.tsv | 1 + ...4_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-01/ses-014/sub-01_ses-014_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-014/anat/sub-01_ses-014_acq-axial_localizer.json create mode 120000 sub-01/ses-014/anat/sub-01_ses-014_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-014/anat/sub-01_ses-014_acq-coronal_localizer.json create mode 120000 sub-01/ses-014/anat/sub-01_ses-014_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-014/anat/sub-01_ses-014_acq-sagittal_localizer.json create mode 120000 sub-01/ses-014/anat/sub-01_ses-014_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-014/anat/sub-01_ses-014_scout.json create mode 120000 sub-01/ses-014/anat/sub-01_ses-014_scout.nii.gz create mode 100644 sub-01/ses-014/fmap/sub-01_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-014/fmap/sub-01_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-014/fmap/sub-01_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-014/fmap/sub-01_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-01/ses-014/sub-01_ses-014_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index bbe7d7850..396ce6f39 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit bbe7d7850d1825f4457f7c9ef101efdd983420f6 +Subproject commit 396ce6f399223e3e7d96e4b1322173088e09e9ee diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-014/anat/sub-01_ses-014_acq-axial_localizer.json b/sub-01/ses-014/anat/sub-01_ses-014_acq-axial_localizer.json new file mode 100644 index 000000000..c9c7b7bb6 --- /dev/null +++ b/sub-01/ses-014/anat/sub-01_ses-014_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:14:2.065000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.261, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0315099, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 248.751 +} \ No newline at end of file diff --git a/sub-01/ses-014/anat/sub-01_ses-014_acq-axial_localizer.nii.gz b/sub-01/ses-014/anat/sub-01_ses-014_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..c4cea9a07 --- /dev/null +++ b/sub-01/ses-014/anat/sub-01_ses-014_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/gp/F6/MD5E-s183243--20cebcaebf9179a70c29d55a53ad84cf.nii.gz/MD5E-s183243--20cebcaebf9179a70c29d55a53ad84cf.nii.gz \ No newline at end of file diff --git a/sub-01/ses-014/anat/sub-01_ses-014_acq-coronal_localizer.json b/sub-01/ses-014/anat/sub-01_ses-014_acq-coronal_localizer.json new file mode 100644 index 000000000..8c2692a41 --- /dev/null +++ b/sub-01/ses-014/anat/sub-01_ses-014_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:14:9.055000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + 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newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..9dd451c44 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.997578, 0.067888, 0.0151211, -0.056996, 0.922538, -0.381673], + 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"ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [622, -7203, -8817, 676, 124, -29, -72, 23], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 248.751, + "dcmmeta_affine": [ + [-1.9951567649841309, -0.11399197578430176, 0.07972152531147003, 109.638671875], + [-0.13577593863010406, 1.8450769186019897, -0.7597737908363342, -59.625244140625], + [0.03024211712181568, 0.7633460164070129, 1.848347544670105, -69.02948760986328], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 52e58475085c5370a218da04f567427eea6a4f45 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:39:50 -0400 Subject: [PATCH 018/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-024_acq-axial_localizer.json | 81 +++ .../sub-01_ses-024_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-024_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-024_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-024_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-024_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-024/anat/sub-01_ses-024_scout.json | 542 ++++++++++++++++++ .../ses-024/anat/sub-01_ses-024_scout.nii.gz | 1 + ...4_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-024_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...24_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...024_task-mario3_run-01_part-mag_events.tsv | 1 + ...024_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...24_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-01_part-phase_events.tsv | 1 + ...4_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-024_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...24_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...024_task-mario3_run-02_part-mag_events.tsv | 1 + ...024_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...24_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-02_part-phase_events.tsv | 1 + ...4_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-024_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...24_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...024_task-mario3_run-03_part-mag_events.tsv | 1 + ...024_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...24_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-03_part-phase_events.tsv | 1 + ...4_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-024_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...24_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...024_task-mario3_run-04_part-mag_events.tsv | 1 + ...024_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...24_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-04_part-phase_events.tsv | 1 + ...4_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-01/ses-024/sub-01_ses-024_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5409 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-024/anat/sub-01_ses-024_acq-axial_localizer.json create mode 120000 sub-01/ses-024/anat/sub-01_ses-024_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-024/anat/sub-01_ses-024_acq-coronal_localizer.json create mode 120000 sub-01/ses-024/anat/sub-01_ses-024_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-024/anat/sub-01_ses-024_acq-sagittal_localizer.json create mode 120000 sub-01/ses-024/anat/sub-01_ses-024_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-024/anat/sub-01_ses-024_scout.json create mode 120000 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participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..4708c7800 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 46 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-024/anat/sub-01_ses-024_acq-axial_localizer.json b/sub-01/ses-024/anat/sub-01_ses-024_acq-axial_localizer.json new file mode 100644 index 000000000..6ea2c9def --- /dev/null +++ b/sub-01/ses-024/anat/sub-01_ses-024_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:37:57.065000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + 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b/sub-01/ses-024/anat/sub-01_ses-024_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..aa383e118 --- /dev/null +++ b/sub-01/ses-024/anat/sub-01_ses-024_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/X5/k9/MD5E-s181040--0d480ccb7fe01ee2b76a9f7f7ba7bc65.nii.gz/MD5E-s181040--0d480ccb7fe01ee2b76a9f7f7ba7bc65.nii.gz \ No newline at end of file diff --git a/sub-01/ses-024/anat/sub-01_ses-024_acq-coronal_localizer.json b/sub-01/ses-024/anat/sub-01_ses-024_acq-coronal_localizer.json new file mode 100644 index 000000000..f2d581bdc --- /dev/null +++ b/sub-01/ses-024/anat/sub-01_ses-024_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:38:4.055000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + 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+../../../.git/annex/objects/4Q/V9/MD5E-s193079--5abbc10cca80273766a7ec5b3a8b48dd.nii.gz/MD5E-s193079--5abbc10cca80273766a7ec5b3a8b48dd.nii.gz \ No newline at end of file diff --git a/sub-01/ses-024/anat/sub-01_ses-024_acq-sagittal_localizer.json b/sub-01/ses-024/anat/sub-01_ses-024_acq-sagittal_localizer.json new file mode 100644 index 000000000..8f5c67c7c --- /dev/null +++ b/sub-01/ses-024/anat/sub-01_ses-024_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:37:50.075000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 0, + 1, + 0, + 0, + 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diff --git a/sub-01/ses-024/anat/sub-01_ses-024_scout.json b/sub-01/ses-024/anat/sub-01_ses-024_scout.json new file mode 100644 index 000000000..20d6a9ba1 --- /dev/null +++ b/sub-01/ses-024/anat/sub-01_ses-024_scout.json @@ -0,0 +1,542 @@ +{ + "AcquisitionMatrixPE": 160, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:37:34.977500", + "BaseResolution": 160, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 5.8e-06, + "EchoTime": 0.00137, + "FlipAngle": 8, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [0, 1, 0, 0, 0, -1], + "ImageOrientationText": "Sag", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "ND", + "NORM" +], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin 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"bd5a98db-3721-4cbd-b0b1-b58f06aa674a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz new file mode 120000 index 000000000..2bb54a28d --- /dev/null +++ b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/gW/Vv/MD5E-s1103747--3c965832ff76fa68b849b48bfa616d6e.nii.gz/MD5E-s1103747--3c965832ff76fa68b849b48bfa616d6e.nii.gz \ No newline at end of file diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-mag_epi.json new file mode 100644 index 000000000..9d028e17d --- /dev/null +++ b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-mag_epi.json @@ -0,0 +1,149 @@ +{ + 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+} \ No newline at end of file diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz new file mode 120000 index 000000000..9ad6c21fe --- /dev/null +++ b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/w0/J5/MD5E-s1115599--b6f73a321ba2552dd720a4cda1971376.nii.gz/MD5E-s1115599--b6f73a321ba2552dd720a4cda1971376.nii.gz \ No newline at end of file diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-phase_epi.json new file mode 100644 index 000000000..a5ce1f7aa --- /dev/null +++ b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-phase_epi.json @@ -0,0 +1,152 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "12:01:33.767500", + 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a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz new file mode 120000 index 000000000..87b068834 --- /dev/null +++ b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/KV/v6/MD5E-s1103550--df6785d41e252280a7c1e2a8365a4f79.nii.gz/MD5E-s1103550--df6785d41e252280a7c1e2a8365a4f79.nii.gz \ No newline at end of file diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_part-mag_epi.json new file mode 100644 index 000000000..dc92a18d3 --- /dev/null +++ b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_part-mag_epi.json @@ -0,0 +1,149 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "12:13:18.467500", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Single-band reference", + "ImageOrientationPatientDICOM": [ + 0.995286, + 0.0931666, + 0.0269544, + -0.07536, + 0.917825, + -0.389766 + ], + "ImageOrientationText": "Tra>Cor(-22.7)>Sag(3.5)", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "ND", + "MOSAIC" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + 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--git a/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_part-phase_bold.nii.gz b/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_part-phase_bold.nii.gz new file mode 120000 index 000000000..5986bea4a --- /dev/null +++ b/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_part-phase_bold.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/kK/XF/MD5E-s335385596--00e7743e5fc87b6609f7623e8fb5a90a.nii.gz/MD5E-s335385596--00e7743e5fc87b6609f7623e8fb5a90a.nii.gz \ No newline at end of file diff --git a/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_part-phase_events.tsv b/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_part-phase_events.tsv new file mode 120000 index 000000000..1bbdfddb5 --- /dev/null +++ b/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_part-phase_events.tsv @@ -0,0 +1 @@ +../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_part-phase_sbref.json b/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_part-phase_sbref.json new file mode 100644 index 000000000..48448abfd --- /dev/null +++ b/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_part-phase_sbref.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "12:13:18.467500", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTime1": 0.037, + "EchoTime2": 0.001, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + 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b/sub-01/ses-024/sub-01_ses-024_scans.tsv new file mode 120000 index 000000000..45c378f11 --- /dev/null +++ b/sub-01/ses-024/sub-01_ses-024_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/9q/9F/MD5E-s3289--05aa4b24106cb6d253882c36da65c176.tsv/MD5E-s3289--05aa4b24106cb6d253882c36da65c176.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..dd377f6ae --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.995286, 0.0931666, 0.0269544, -0.07536, 0.917825, -0.389766], + "ImageOrientationText": "Tra>Cor(-22.7)>Sag(3.5)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0837087, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [600, -7232, -8821, 608, 110, -50, -129, 82], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 310.44, + "dcmmeta_affine": [ + [-1.9905712604522705, -0.15072008967399597, 0.12210506200790405, 111.7552490234375], + [-0.18633314967155457, 1.83565092086792, -0.7717939019203186, -56.160953521728516], + [0.053908709436655045, 0.7795314788818359, 1.8410390615463257, -71.87001037597656], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From c7754846e3cdec077594177ffb8a59aa78cdbee5 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:40:38 -0400 Subject: [PATCH 019/463] fix fmap phase --- ...1_ses-007_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-007_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-007_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-007_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-007_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - sub-01/ses-007/sub-01_ses-007_scans.tsv | 2 +- 17 files changed, 1 insertion(+), 638 deletions(-) rename sub-01/ses-007/fmap/{sub-01_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-007_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-007/fmap/{sub-01_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-007_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-007/fmap/{sub-01_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-007_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-007/fmap/{sub-01_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-007_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-007/fmap/{sub-01_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-007_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-007/fmap/{sub-01_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-007_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-007/fmap/{sub-01_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-007_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-007/fmap/{sub-01_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-007_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 1d0b8623f..000000000 --- a/sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:40:46.565000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - 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"114048.055000", "114049.545000"], - "ContentTime": ["114132.584000", "114132.587000", "114132.589000"], - "InstanceCreationTime": ["114132.584000", "114132.587000", "114132.589000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4822.0, 4850.0, 4856.0], - "WindowWidth": [18648.0, 18686.0, 18686.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 7882d9631..000000000 --- a/sub-01/ses-007/fmap/sub-01_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/67/xG/MD5E-s3334842--4dd82caa91da2a9eb72111dc6b02ef49.nii.gz/MD5E-s3334842--4dd82caa91da2a9eb72111dc6b02ef49.nii.gz \ No newline at end of file diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index f28c616da..000000000 --- a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - 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r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 4413511d4..000000000 --- a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/0K/zp/MD5E-s1112293--78fc0f6ea23abef8b12eaa6dfc2894af.nii.gz/MD5E-s1112293--78fc0f6ea23abef8b12eaa6dfc2894af.nii.gz \ No newline at end of file diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index ed9d7f6a7..000000000 --- a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:42:44.842500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993334, - 0.114646, - 0.0119647, - -0.100374, - 0.911342, - -0.399225 - ], - "ImageOrientationText": "Tra>Cor(-23.3)>Sag(3.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": 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0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 294.962, - "WipMemBlock": "1c047bb1-5073-40dc-96af-0a796684c9f9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 29fda8f10..000000000 --- a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/jF/zj/MD5E-s1103669--aec2f3bf2d0689f793e72551c867b2a6.nii.gz/MD5E-s1103669--aec2f3bf2d0689f793e72551c867b2a6.nii.gz \ No newline at end of file diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index e871aef80..000000000 --- a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:51:49.537500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993334, - 0.114646, - 0.0119647, - -0.100374, - 0.911342, - -0.399225 - ], - "ImageOrientationText": "Tra>Cor(-23.3)>Sag(3.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0647014, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 622, - -7196, - -8815, - 629, - 86, - 26, - -82, - 9 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 294.962, - "WipMemBlock": "c9df3d6f-93f1-4d38-b22f-6676d9684027||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index d8bb4340b..000000000 --- a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Gx/F7/MD5E-s1103659--32961c13003dfa18128ed9228422f76e.nii.gz/MD5E-s1103659--32961c13003dfa18128ed9228422f76e.nii.gz \ No newline at end of file diff --git a/sub-01/ses-007/sub-01_ses-007_scans.tsv b/sub-01/ses-007/sub-01_ses-007_scans.tsv index 468cb4e8f..3d0ded2c4 120000 --- a/sub-01/ses-007/sub-01_ses-007_scans.tsv +++ b/sub-01/ses-007/sub-01_ses-007_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/G8/84/MD5E-s2045--41dc0da475790eccee63bb0d156dffa0.tsv/MD5E-s2045--41dc0da475790eccee63bb0d156dffa0.tsv \ No newline at end of file +../../.git/annex/objects/Pf/J7/MD5E-s1565--ed773f48d61827cabec716e141107258.tsv/MD5E-s1565--ed773f48d61827cabec716e141107258.tsv \ No newline at end of file From cb37194fe753c995c131b46c00cc512c967f5360 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:40:45 -0400 Subject: [PATCH 020/463] fix fmap phase --- ...1_ses-016_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-016_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-016_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-016_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-016_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-016_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-01/ses-016/sub-01_ses-016_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-01/ses-016/fmap/{sub-01_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-016_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-016/fmap/{sub-01_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-016_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-016/fmap/{sub-01_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-016_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-016/fmap/{sub-01_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-016_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-016/fmap/{sub-01_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-016_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-016/fmap/{sub-01_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-016_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-016/fmap/{sub-01_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-016_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-016/fmap/{sub-01_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-016_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-01/ses-016/fmap/{sub-01_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-01_ses-016_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-01/ses-016/fmap/{sub-01_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-01_ses-016_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 559604694..000000000 --- a/sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "17:14:41.415000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.993461, 0.112918, 0.0169013, -0.0984601, 0.922226, -0.373904], - "ImageOrientationText": "Tra>Cor(-21.7)>Sag(3.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0379319, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [618, -7207, -8804, 658, 99, -29, -55, 22], - "SliceThickness": 2, - "SliceTiming": [0, 0.7825, 0.0975, 0.88, 0.195, 0.9775, 0.2925, 1.0775, 0.39, 1.175, 0.49, 1.2725, 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0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99346059042697, 0.11291767894472, 0.01690127362764, -0.098460058624, 0.9222262356434, -0.3739042486343], - "ImagePositionPatient": [-743.06409630109, -888.05764427069, 272.31499029646], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.260239, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "171248.602000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.03793187828085, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "171527.969000", - "SliceLocation": -32.92354180599, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000371414, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "171248.538000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["171441.415000", "171442.905000", "171444.395000"], - "ContentTime": ["171527.971000", "171527.973000", "171527.976000"], - "InstanceCreationTime": ["171527.971000", "171527.973000", "171527.976000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4790.0, 4790.0, 4764.0], - "WindowWidth": [18570.0, 18568.0, 18534.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index edb14852b..000000000 --- a/sub-01/ses-016/fmap/sub-01_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/zp/kz/MD5E-s3335265--7578078d11a4c9d04f8bc6b81bbc0538.nii.gz/MD5E-s3335265--7578078d11a4c9d04f8bc6b81bbc0538.nii.gz \ No newline at end of file diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 1c69e12dd..000000000 --- a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "17:14:30.985000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993461, - 0.112918, - 0.0169013, - -0.0984601, - 0.922226, - -0.373904 - ], - "ImageOrientationText": "Tra>Cor(-21.7)>Sag(3.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0379319, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 618, - -7207, - -8804, - 658, - 99, - -29, - -55, - 22 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 254.136, - "WipMemBlock": "e4bb647e-1113-4660-aaf1-0cb335f9678d||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 6279b4453..000000000 --- a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/K6/FV/MD5E-s1112289--ac8f3b40ee9f6dbc3099f9fe7390327a.nii.gz/MD5E-s1112289--ac8f3b40ee9f6dbc3099f9fe7390327a.nii.gz \ No newline at end of file diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 4cb9431fb..000000000 --- a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "17:18:18.725000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993461, - 0.112918, - 0.0169013, - -0.0984601, - 0.922226, - -0.373904 - ], - "ImageOrientationText": "Tra>Cor(-21.7)>Sag(3.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0475633, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 618, - -7207, - -8804, - 658, - 99, - -29, - -55, - 22 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 254.136, - "WipMemBlock": "5fa652c7-142f-41c6-880b-50e0562dcdf1||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index ebc9f7466..000000000 --- a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3W/9K/MD5E-s1103759--1069717093fe2e298b59f0fca6616833.nii.gz/MD5E-s1103759--1069717093fe2e298b59f0fca6616833.nii.gz \ No newline at end of file diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 74e051014..000000000 --- a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "17:27:34.342500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of 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"MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0475633, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 618, - -7207, - -8804, - 658, - 99, - -29, - -55, - 22 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 254.136, - "WipMemBlock": "d09057cb-602f-44d9-8e06-0df568da920c||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 1d35c7820..000000000 --- a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/96/6P/MD5E-s1103920--5591fe5d55eba61e1b75b2a1d851caa7.nii.gz/MD5E-s1103920--5591fe5d55eba61e1b75b2a1d851caa7.nii.gz \ No newline at end of file diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 51095a612..000000000 --- a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "17:38:3.235000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993461, - 0.112918, - 0.0169013, - -0.0984601, - 0.922226, - -0.373904 - ], - "ImageOrientationText": "Tra>Cor(-21.7)>Sag(3.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0475633, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 618, - -7207, - -8804, - 658, - 99, - -29, - -55, - 22 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 254.136, - "WipMemBlock": "e661d058-5893-4e82-9001-2a3414cf6a9c||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 0d3e4061a..000000000 --- a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/7V/11/MD5E-s1103908--67f790c19922fb2b7d95b2e2114ef168.nii.gz/MD5E-s1103908--67f790c19922fb2b7d95b2e2114ef168.nii.gz \ No newline at end of file diff --git a/sub-01/ses-016/sub-01_ses-016_scans.tsv b/sub-01/ses-016/sub-01_ses-016_scans.tsv index ae0f546fc..f55befe56 120000 --- a/sub-01/ses-016/sub-01_ses-016_scans.tsv +++ b/sub-01/ses-016/sub-01_ses-016_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/QW/K2/MD5E-s2667--56397133c99ddbb0cf7f139c83c8b286.tsv/MD5E-s2667--56397133c99ddbb0cf7f139c83c8b286.tsv \ No newline at end of file +../../.git/annex/objects/mx/g1/MD5E-s2066--32cde005a62cd420dff6275a61a030e3.tsv/MD5E-s2066--32cde005a62cd420dff6275a61a030e3.tsv \ No newline at end of file From e7acaafd169e9325d0215d1470a8aa5335ffe0a9 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:40:54 -0400 Subject: [PATCH 021/463] fix complex event files --- ...g_events.tsv => sub-01_ses-007_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-007_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-007_task-mario3_run-02_part-mag_events.tsv | 1 - .../func/sub-01_ses-007_task-mario3_run-02_part-phase_events.tsv | 1 - 4 files changed, 2 deletions(-) rename sub-01/ses-007/func/{sub-01_ses-007_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-007_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-007/func/{sub-01_ses-007_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-007_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-mag_events.tsv delete mode 120000 sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-phase_events.tsv diff --git a/sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-007/func/sub-01_ses-007_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 99b532445801d9cc527b7e815f2bd6265cd8c21c Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:40:59 -0400 Subject: [PATCH 022/463] fix fmap phase --- ...1_ses-014_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-014_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-014_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-014_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-014_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-014_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-01/ses-014/sub-01_ses-014_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-01/ses-014/fmap/{sub-01_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-014_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-014/fmap/{sub-01_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-014_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-014/fmap/sub-01_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-014/fmap/sub-01_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-014/fmap/{sub-01_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-014_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-014/fmap/{sub-01_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-014_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-014/fmap/{sub-01_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-014_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-014/fmap/{sub-01_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-014_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-014/fmap/{sub-01_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-014_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-014/fmap/{sub-01_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-014_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-01/ses-014/fmap/{sub-01_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-01_ses-014_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-01/ses-014/fmap/{sub-01_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-01_ses-014_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-014/fmap/sub-01_ses-014_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-014/fmap/sub-01_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-014/fmap/sub-01_ses-014_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-014/fmap/sub-01_ses-014_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-014/fmap/sub-01_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-014/fmap/sub-01_ses-014_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-014/fmap/sub-01_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 046d9751b..000000000 --- a/sub-01/ses-014/fmap/sub-01_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:15:9.672500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.997578, 0.067888, 0.0151211, -0.056996, 0.922538, -0.381673], - "ImageOrientationText": "Tra>Cor(-22.3)>Sag(2.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0370129, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [622, -7203, -8817, 676, 124, -29, -72, 23], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.08, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875, 0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.08, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875, 0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.08, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875, 0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.08, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 248.751, - "WipMemBlock": "d748f680-0346-4b07-8230-2627bab322fc||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9951567649841309, -0.11399197578430176, 0.07972152531147003, 109.638671875], - [-0.13577593863010406, 1.8450769186019897, -0.7597737908363342, -59.625244140625], - [0.03024211712181568, 0.7633460164070129, 1.848347544670105, -69.02948760986328], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 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sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 51ea77700..000000000 --- a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:14:59.242500", - "BandwidthPerPixelPhaseEncode": 17.17, - 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a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index a15d72052..000000000 --- a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/VV/x3/MD5E-s1112281--4148ba6451edef6149cfe9a971f303e3.nii.gz/MD5E-s1112281--4148ba6451edef6149cfe9a971f303e3.nii.gz \ No newline at end of file diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 85095b5a6..000000000 --- a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:16:24.497500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - 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a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/4V/Xp/MD5E-s1103926--82b052dddd8cba490b7c3344c3701c61.nii.gz/MD5E-s1103926--82b052dddd8cba490b7c3344c3701c61.nii.gz \ No newline at end of file diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 8314e7d6d..000000000 --- a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:26:29.297500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": 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"ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.046411, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 622, - -7203, - -8817, - 676, - 124, - -29, - -72, - 23 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 248.751, - "WipMemBlock": "0a1188a5-603e-4fe0-8ff4-738f76f30ff1||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 1bb8d42b4..000000000 --- a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/1V/z8/MD5E-s1104030--8a12d0321df0513b75211732c1a07955.nii.gz/MD5E-s1104030--8a12d0321df0513b75211732c1a07955.nii.gz \ No newline at end of file diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index fd9be1835..000000000 --- a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:38:6.405000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997578, - 0.067888, - 0.0151211, - -0.056996, - 0.922538, - -0.381673 - ], - "ImageOrientationText": "Tra>Cor(-22.3)>Sag(2.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.046411, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 622, - -7203, - -8817, - 676, - 124, - -29, - -72, - 23 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 248.751, - "WipMemBlock": "61588a62-0244-4d1a-a50a-17231509f8a0||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index ead7f2910..000000000 --- a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/p6/MW/MD5E-s1103941--cd9e4bcc993fb5616727f9df1310da55.nii.gz/MD5E-s1103941--cd9e4bcc993fb5616727f9df1310da55.nii.gz \ No newline at end of file diff --git a/sub-01/ses-014/sub-01_ses-014_scans.tsv b/sub-01/ses-014/sub-01_ses-014_scans.tsv index f9f64d35c..802707dba 120000 --- a/sub-01/ses-014/sub-01_ses-014_scans.tsv +++ b/sub-01/ses-014/sub-01_ses-014_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/jW/vP/MD5E-s2667--c09c236dcf3ef28ecfe2fa48e641ae36.tsv/MD5E-s2667--c09c236dcf3ef28ecfe2fa48e641ae36.tsv \ No newline at end of file +../../.git/annex/objects/gM/gq/MD5E-s2066--ec6270053a3371d31481816b56c21ba8.tsv/MD5E-s2066--ec6270053a3371d31481816b56c21ba8.tsv \ No newline at end of file From b654c968c827d7681d78bd6a83be4baef0607f4e Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:41:15 -0400 Subject: [PATCH 023/463] fix complex event files --- ...g_events.tsv => sub-01_ses-016_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-016_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-016_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-01_ses-016_task-mario3_run-03_events.tsv} | 0 .../func/sub-01_ses-016_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-01_ses-016_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-01/ses-016/func/{sub-01_ses-016_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-016_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-016/func/{sub-01_ses-016_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-016_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-02_part-phase_events.tsv rename sub-01/ses-016/func/{sub-01_ses-016_task-mario3_run-02_part-mag_events.tsv => sub-01_ses-016_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_events.tsv similarity index 100% rename from sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-02_part-mag_events.tsv rename to sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_events.tsv diff --git a/sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_part-mag_events.tsv b/sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-016/func/sub-01_ses-016_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 008b0a9d690bf3ce15c5801407f4f53ef5656c25 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:41:33 -0400 Subject: [PATCH 024/463] fix complex event files --- ...g_events.tsv => sub-01_ses-014_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-014_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-014_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-01_ses-014_task-mario3_run-03_events.tsv} | 0 .../func/sub-01_ses-014_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-01_ses-014_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-01/ses-014/func/{sub-01_ses-014_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-014_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-014/func/{sub-01_ses-014_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-014_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-02_part-phase_events.tsv rename sub-01/ses-014/func/{sub-01_ses-014_task-mario3_run-02_part-mag_events.tsv => sub-01_ses-014_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_events.tsv similarity index 100% rename from sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-02_part-mag_events.tsv rename to sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_events.tsv diff --git a/sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_part-mag_events.tsv b/sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-014/func/sub-01_ses-014_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From a578e87ae7e1adc78fc90a94e03196254e1c8790 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:41:40 -0400 Subject: [PATCH 025/463] fix fmap phase --- ...1_ses-024_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-024_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-024_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-024_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-024_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-024_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-024_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-024_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-024_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-024_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-024_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-024_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-01/ses-024/sub-01_ses-024_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-01/ses-024/fmap/{sub-01_ses-024_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-024_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-024/fmap/{sub-01_ses-024_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-024_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-024/fmap/sub-01_ses-024_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-024/fmap/sub-01_ses-024_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-024/fmap/{sub-01_ses-024_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-024_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-024/fmap/{sub-01_ses-024_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-024_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-024/fmap/{sub-01_ses-024_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-024_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-024/fmap/{sub-01_ses-024_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-024_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-024/fmap/{sub-01_ses-024_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-024_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-024/fmap/{sub-01_ses-024_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-024_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-01/ses-024/fmap/{sub-01_ses-024_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-01_ses-024_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-01/ses-024/fmap/{sub-01_ses-024_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-01_ses-024_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-01/ses-024/fmap/{sub-01_ses-024_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-01_ses-024_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-01/ses-024/fmap/{sub-01_ses-024_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-01_ses-024_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-024/fmap/sub-01_ses-024_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-024/fmap/sub-01_ses-024_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-024/fmap/sub-01_ses-024_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-024/fmap/sub-01_ses-024_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-024/fmap/sub-01_ses-024_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 7f0e6b6d1..000000000 --- a/sub-01/ses-024/fmap/sub-01_ses-024_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:39:10.400000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.995286, 0.0931666, 0.0269544, -0.07536, 0.917825, -0.389766], - "ImageOrientationText": "Tra>Cor(-22.7)>Sag(3.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - 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[0.053908709436655045, 0.7795314788818359, 1.8410390615463257, -71.87001037597656], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99528561336371, 0.09316657464484, 0.02695435401141, -0.0753600455196, 0.91782544167288, -0.3897657272738], - "ImagePositionPatient": [-765.93689579338, -868.91327711675, 272.54841268247], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.25909, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "113637.223000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.06675801643327, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "113957.670000", - "SliceLocation": -37.662462208175, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000501357, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "113637.147000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["113910.400000", "113911.890000", "113913.380000"], - "ContentTime": ["113957.672000", "113957.675000", "113957.677000"], - "InstanceCreationTime": ["113957.672000", "113957.675000", "113957.677000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4822.0, 4822.0, 4824.0], - "WindowWidth": [18650.0, 18648.0, 18646.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-024/fmap/sub-01_ses-024_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 42efc2992..000000000 --- a/sub-01/ses-024/fmap/sub-01_ses-024_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Xj/98/MD5E-s3334681--90888e67bebecc558ccafd7c8e82f584.nii.gz/MD5E-s3334681--90888e67bebecc558ccafd7c8e82f584.nii.gz \ No newline at end of file diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index f570fb229..000000000 --- a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:38:59.970000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995286, - 0.0931666, - 0.0269544, - -0.07536, - 0.917825, - -0.389766 - ], - "ImageOrientationText": "Tra>Cor(-22.7)>Sag(3.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.066758, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 600, - -7232, - -8821, - 608, - 110, - -50, - -129, - 82 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 310.44, - "WipMemBlock": "f7fe520d-b662-40c4-bb00-d002387aa2ef||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 3536895d0..000000000 --- a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/P9/6f/MD5E-s1112403--50e52d345978a85b4e9e5c3c907d35e1.nii.gz/MD5E-s1112403--50e52d345978a85b4e9e5c3c907d35e1.nii.gz \ No newline at end of file diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 56268fe93..000000000 --- a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:40:1.942500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 310.44, - "WipMemBlock": "54ccbad0-f05b-40bd-ae7d-5225e59c4a4f||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 0354c4275..000000000 --- a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Fq/VM/MD5E-s1103628--fb769ae44f76a7ab1dbc37d92760a3d7.nii.gz/MD5E-s1103628--fb769ae44f76a7ab1dbc37d92760a3d7.nii.gz \ No newline at end of file diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 4ea0ce8db..000000000 --- a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:50:1.575000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995286, - 0.0931666, - 0.0269544, - -0.07536, - 0.917825, - -0.389766 - ], - "ImageOrientationText": "Tra>Cor(-22.7)>Sag(3.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0837087, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 600, - -7232, - -8821, - 608, - 110, - -50, - -129, - 82 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 310.44, - "WipMemBlock": "bd5a98db-3721-4cbd-b0b1-b58f06aa674a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 2bb54a28d..000000000 --- a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/gW/Vv/MD5E-s1103747--3c965832ff76fa68b849b48bfa616d6e.nii.gz/MD5E-s1103747--3c965832ff76fa68b849b48bfa616d6e.nii.gz \ No newline at end of file diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index a5ce1f7aa..000000000 --- a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "12:01:33.767500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995286, - 0.0931666, - 0.0269544, - -0.07536, - 0.917825, - -0.389766 - ], - "ImageOrientationText": "Tra>Cor(-22.7)>Sag(3.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0837087, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 600, - -7232, - -8821, - 608, - 110, - -50, - -129, - 82 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 310.44, - "WipMemBlock": "9e10c426-8ec8-4fba-a96e-f4839da72bcd||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 87b068834..000000000 --- a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/KV/v6/MD5E-s1103550--df6785d41e252280a7c1e2a8365a4f79.nii.gz/MD5E-s1103550--df6785d41e252280a7c1e2a8365a4f79.nii.gz \ No newline at end of file diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index e5d68e6b1..000000000 --- a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "12:13:18.467500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995286, - 0.0931666, - 0.0269544, - -0.07536, - 0.917825, - -0.389766 - ], - "ImageOrientationText": "Tra>Cor(-22.7)>Sag(3.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0837087, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 600, - -7232, - -8821, - 608, - 110, - -50, - -129, - 82 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 310.44, - "WipMemBlock": "e774e0f3-bde6-4f6d-97e1-a7cd09c4338e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index b7c70c132..000000000 --- a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/M0/0G/MD5E-s1103784--0216c04dcd8ab9dabbe0a922210283b0.nii.gz/MD5E-s1103784--0216c04dcd8ab9dabbe0a922210283b0.nii.gz \ No newline at end of file diff --git a/sub-01/ses-024/sub-01_ses-024_scans.tsv b/sub-01/ses-024/sub-01_ses-024_scans.tsv index 45c378f11..463294291 120000 --- a/sub-01/ses-024/sub-01_ses-024_scans.tsv +++ b/sub-01/ses-024/sub-01_ses-024_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/9q/9F/MD5E-s3289--05aa4b24106cb6d253882c36da65c176.tsv/MD5E-s3289--05aa4b24106cb6d253882c36da65c176.tsv \ No newline at end of file +../../.git/annex/objects/WW/0p/MD5E-s2567--e25b62a8b0b7ea6b859a40704389a962.tsv/MD5E-s2567--e25b62a8b0b7ea6b859a40704389a962.tsv \ No newline at end of file From 227419aeba1349f60a611e561b8c3274b4d1522f Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:41:56 -0400 Subject: [PATCH 026/463] fill IntendedFor --- ...1_ses-007_acq-sbref_dir-AP_run-01_epi.json | 89 ++----------------- ...1_ses-007_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-007_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- 3 files changed, 22 insertions(+), 243 deletions(-) diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_epi.json index 5bfe472e5..c87bb08d7 100644 --- a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993334, - 0.114646, - 0.0119647, - -0.100374, - 0.911342, - -0.399225 - ], + "ImageOrientationPatientDICOM": [0.993334, 0.114646, 0.0119647, -0.100374, 0.911342, -0.399225], "ImageOrientationText": "Tra>Cor(-23.3)>Sag(3.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,16 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-01_ses-007_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-007/func/sub-01_ses-007_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +64,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 622, - -7196, - -8815, - 629, - 86, - 26, - -82, - 9 - ], + "ShimSetting": [622, -7196, -8815, 629, 86, 26, -82, 9], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.9775, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_epi.json index f8afa6f69..3063c7c2d 100644 --- a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993334, - 0.114646, - 0.0119647, - -0.100374, - 0.911342, - -0.399225 - ], + "ImageOrientationPatientDICOM": [0.993334, 0.114646, 0.0119647, -0.100374, 0.911342, -0.399225], "ImageOrientationText": "Tra>Cor(-23.3)>Sag(3.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-01_ses-007_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 622, - -7196, - -8815, - 629, - 86, - 26, - -82, - 9 - ], + "ShimSetting": [622, -7196, -8815, 629, 86, 26, -82, 9], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_epi.json index 61502e96b..5aa842eb6 100644 --- a/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-007/fmap/sub-01_ses-007_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993334, - 0.114646, - 0.0119647, - -0.100374, - 0.911342, - -0.399225 - ], + "ImageOrientationPatientDICOM": [0.993334, 0.114646, 0.0119647, -0.100374, 0.911342, -0.399225], "ImageOrientationText": "Tra>Cor(-23.3)>Sag(3.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-01_ses-007_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 622, - -7196, - -8815, - 629, - 86, - 26, - -82, - 9 - ], + "ShimSetting": [622, -7196, -8815, 629, 86, 26, -82, 9], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 3fbb242576b0f30258d04c344b719d19b5dab003 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:42:00 -0400 Subject: [PATCH 027/463] fill IntendedFor --- ...1_ses-016_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...1_ses-016_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-016_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...1_ses-016_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_epi.json index 1ec3d4043..f89a6441b 100644 --- a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993461, - 0.112918, - 0.0169013, - -0.0984601, - 0.922226, - -0.373904 - ], + "ImageOrientationPatientDICOM": [0.993461, 0.112918, 0.0169013, -0.0984601, 0.922226, -0.373904], "ImageOrientationText": "Tra>Cor(-21.7)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-01_ses-016_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-016/func/sub-01_ses-016_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-016/func/sub-01_ses-016_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 618, - -7207, - -8804, - 658, - 99, - -29, - -55, - 22 - ], + "ShimSetting": [618, -7207, -8804, 658, 99, -29, -55, 22], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.9775, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_epi.json index c5100946a..81338e64e 100644 --- a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993461, - 0.112918, - 0.0169013, - -0.0984601, - 0.922226, - -0.373904 - ], + "ImageOrientationPatientDICOM": [0.993461, 0.112918, 0.0169013, -0.0984601, 0.922226, -0.373904], "ImageOrientationText": "Tra>Cor(-21.7)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-01_ses-016_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 618, - -7207, - -8804, - 658, - 99, - -29, - -55, - 22 - ], + "ShimSetting": [618, -7207, -8804, 658, 99, -29, -55, 22], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_epi.json index 28913e40d..bdab7d732 100644 --- a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993461, - 0.112918, - 0.0169013, - -0.0984601, - 0.922226, - -0.373904 - ], + "ImageOrientationPatientDICOM": [0.993461, 0.112918, 0.0169013, -0.0984601, 0.922226, -0.373904], "ImageOrientationText": "Tra>Cor(-21.7)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-01_ses-016_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 618, - -7207, - -8804, - 658, - 99, - -29, - -55, - 22 - ], + "ShimSetting": [618, -7207, -8804, 658, 99, -29, -55, 22], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_epi.json b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_epi.json index 457b3c243..1b5d367c1 100644 --- a/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-01/ses-016/fmap/sub-01_ses-016_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993461, - 0.112918, - 0.0169013, - -0.0984601, - 0.922226, - -0.373904 - ], + "ImageOrientationPatientDICOM": [0.993461, 0.112918, 0.0169013, -0.0984601, 0.922226, -0.373904], "ImageOrientationText": "Tra>Cor(-21.7)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-01_ses-016_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 618, - -7207, - -8804, - 658, - 99, - -29, - -55, - 22 - ], + "ShimSetting": [618, -7207, -8804, 658, 99, -29, -55, 22], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 084c79b65ddd56a0f05d1385b2d75b4837bbb20f Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:42:03 -0400 Subject: [PATCH 028/463] fill IntendedFor --- ...1_ses-014_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...1_ses-014_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-014_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...1_ses-014_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_epi.json index b74bff89b..c65125b42 100644 --- a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997578, - 0.067888, - 0.0151211, - -0.056996, - 0.922538, - -0.381673 - ], + "ImageOrientationPatientDICOM": [0.997578, 0.067888, 0.0151211, -0.056996, 0.922538, -0.381673], "ImageOrientationText": "Tra>Cor(-22.3)>Sag(2.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-01_ses-014_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-014/func/sub-01_ses-014_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-014/func/sub-01_ses-014_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 622, - -7203, - -8817, - 676, - 124, - -29, - -72, - 23 - ], + "ShimSetting": [622, -7203, -8817, 676, 124, -29, -72, 23], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_epi.json index ffb0dd49f..57a2dce2f 100644 --- a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997578, - 0.067888, - 0.0151211, - -0.056996, - 0.922538, - -0.381673 - ], + "ImageOrientationPatientDICOM": [0.997578, 0.067888, 0.0151211, -0.056996, 0.922538, -0.381673], "ImageOrientationText": "Tra>Cor(-22.3)>Sag(2.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-01_ses-014_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 622, - -7203, - -8817, - 676, - 124, - -29, - -72, - 23 - ], + "ShimSetting": [622, -7203, -8817, 676, 124, -29, -72, 23], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_epi.json index 34f4bfd94..40722f7bc 100644 --- a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997578, - 0.067888, - 0.0151211, - -0.056996, - 0.922538, - -0.381673 - ], + "ImageOrientationPatientDICOM": [0.997578, 0.067888, 0.0151211, -0.056996, 0.922538, -0.381673], "ImageOrientationText": "Tra>Cor(-22.3)>Sag(2.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-01_ses-014_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 622, - -7203, - -8817, - 676, - 124, - -29, - -72, - 23 - ], + "ShimSetting": [622, -7203, -8817, 676, 124, -29, -72, 23], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_epi.json b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_epi.json index d4a737361..3eef735f5 100644 --- a/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-01/ses-014/fmap/sub-01_ses-014_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997578, - 0.067888, - 0.0151211, - -0.056996, - 0.922538, - -0.381673 - ], + "ImageOrientationPatientDICOM": [0.997578, 0.067888, 0.0151211, -0.056996, 0.922538, -0.381673], "ImageOrientationText": "Tra>Cor(-22.3)>Sag(2.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-01_ses-014_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 622, - -7203, - -8817, - 676, - 124, - -29, - -72, - 23 - ], + "ShimSetting": [622, -7203, -8817, 676, 124, -29, -72, 23], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 4e1fd7d46e2c35fd5f5263fcfecd7bfef3f58379 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:42:14 -0400 Subject: [PATCH 029/463] fix complex event files --- ...g_events.tsv => sub-01_ses-024_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-024_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-01_ses-024_task-mario3_run-03_events.tsv} | 0 .../func/sub-01_ses-024_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-01_ses-024_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-01_ses-024_task-mario3_run-04_events.tsv} | 0 .../func/sub-01_ses-024_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-01_ses-024_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-01/ses-024/func/{sub-01_ses-024_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-024_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-024/func/{sub-01_ses-024_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-024_task-mario3_run-02_events.tsv} (100%) rename sub-01/ses-024/func/{sub-01_ses-024_task-mario3_run-02_part-mag_events.tsv => sub-01_ses-024_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-03_part-phase_events.tsv rename sub-01/ses-024/func/{sub-01_ses-024_task-mario3_run-02_part-phase_events.tsv => sub-01_ses-024_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-03_events.tsv similarity index 100% rename from sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-02_part-mag_events.tsv rename to sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-03_events.tsv diff --git a/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-03_part-mag_events.tsv b/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_events.tsv similarity index 100% rename from sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-02_part-phase_events.tsv rename to sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_events.tsv diff --git a/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_part-mag_events.tsv b/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_part-phase_events.tsv b/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 147c558878a0abf445981c164f282929b3627771 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:42:27 -0400 Subject: [PATCH 030/463] fill IntendedFor --- ...1_ses-024_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...1_ses-024_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-024_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...1_ses-024_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...1_ses-024_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_epi.json index 3c7cf133e..bc123daf8 100644 --- a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995286, - 0.0931666, - 0.0269544, - -0.07536, - 0.917825, - -0.389766 - ], + "ImageOrientationPatientDICOM": [0.995286, 0.0931666, 0.0269544, -0.07536, 0.917825, -0.389766], "ImageOrientationText": "Tra>Cor(-22.7)>Sag(3.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-024/func/sub-01_ses-024_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-024/func/sub-01_ses-024_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-024/func/sub-01_ses-024_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-024/func/sub-01_ses-024_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 600, - -7232, - -8821, - 608, - 110, - -50, - -129, - 82 - ], + "ShimSetting": [600, -7232, -8821, 608, 110, -50, -129, 82], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_epi.json index 223209d5d..2dd8b6b63 100644 --- a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995286, - 0.0931666, - 0.0269544, - -0.07536, - 0.917825, - -0.389766 - ], + "ImageOrientationPatientDICOM": [0.995286, 0.0931666, 0.0269544, -0.07536, 0.917825, -0.389766], "ImageOrientationText": "Tra>Cor(-22.7)>Sag(3.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-024/func/sub-01_ses-024_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 600, - -7232, - -8821, - 608, - 110, - -50, - -129, - 82 - ], + "ShimSetting": [600, -7232, -8821, 608, 110, -50, -129, 82], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_epi.json index cd3530f55..5fac0e1fe 100644 --- a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995286, - 0.0931666, - 0.0269544, - -0.07536, - 0.917825, - -0.389766 - ], + "ImageOrientationPatientDICOM": [0.995286, 0.0931666, 0.0269544, -0.07536, 0.917825, -0.389766], "ImageOrientationText": "Tra>Cor(-22.7)>Sag(3.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-024/func/sub-01_ses-024_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 600, - -7232, - -8821, - 608, - 110, - -50, - -129, - 82 - ], + "ShimSetting": [600, -7232, -8821, 608, 110, -50, -129, 82], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_epi.json index 9d028e17d..40a2e31c0 100644 --- a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995286, - 0.0931666, - 0.0269544, - -0.07536, - 0.917825, - -0.389766 - ], + "ImageOrientationPatientDICOM": [0.995286, 0.0931666, 0.0269544, -0.07536, 0.917825, -0.389766], "ImageOrientationText": "Tra>Cor(-22.7)>Sag(3.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-024/func/sub-01_ses-024_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 600, - -7232, - -8821, - 608, - 110, - -50, - -129, - 82 - ], + "ShimSetting": [600, -7232, -8821, 608, 110, -50, -129, 82], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_epi.json b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_epi.json index dc92a18d3..71dcaf703 100644 --- a/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-01/ses-024/fmap/sub-01_ses-024_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995286, - 0.0931666, - 0.0269544, - -0.07536, - 0.917825, - -0.389766 - ], + "ImageOrientationPatientDICOM": [0.995286, 0.0931666, 0.0269544, -0.07536, 0.917825, -0.389766], "ImageOrientationText": "Tra>Cor(-22.7)>Sag(3.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-024/func/sub-01_ses-024_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 600, - -7232, - -8821, - 608, - 110, - -50, - -129, - 82 - ], + "ShimSetting": [600, -7232, -8821, 608, 110, -50, -129, 82], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 921216ee54b1f3a33320260e393b2edefecf2bb9 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:46:43 -0400 Subject: [PATCH 031/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..bfe5cf55b --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 931dfecf-0467-4946-931b-217c8747e87d diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..57c079c68 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 57c079c689ac463d492dd48539ba817f5ebc22de From 1e6375a1c99c7f321a2955c2af46f70bf94d3787 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:48:10 -0400 Subject: [PATCH 032/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..08641f20b --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 0d0a5db2-5e69-4102-836b-93cba5418dcd diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..8f66f116c --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 8f66f116cda552f24480c3ca773ae82d059e86c8 From d9431ae23ce693351fdc62d5632ebcc7dc12d3f7 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:49:50 -0400 Subject: [PATCH 033/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..d92442ef6 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 890e139f-4698-421e-83fc-39415727df25 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..bece9b3a0 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit bece9b3a08a756313ddc18e62e24d2d12c5df6cc From 7c8e05f947fe7852de0ed75c0b40f991431afab3 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:50:23 -0400 Subject: [PATCH 034/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..071b9a555 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 9ae2f411-dd54-4561-bcbc-162e33efd943 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..f2b71fc6a --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit f2b71fc6a7fabff77091f4d0dd89e1f678cf29c4 From 74111278c4bd0526e0027b7034119abcfba5e5cd Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:51:49 -0400 Subject: [PATCH 035/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..c3c4619e7 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 03d862c1-ea6b-4915-befe-b358ad0bd84c diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..a165b19b2 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit a165b19b23509af4683e378494dbed466f2e50c1 From 1ab43f9c0bbe92bc2a927a5df95bd769b55980b0 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:54:39 -0400 Subject: [PATCH 036/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-005_acq-axial_localizer.json | 81 +++ .../sub-01_ses-005_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-005_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-005_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-005_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-005_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-005/anat/sub-01_ses-005_scout.json | 542 ++++++++++++++++++ .../ses-005/anat/sub-01_ses-005_scout.nii.gz | 1 + ...5_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ...-005_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...05_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...005_task-mario3_run-01_part-mag_events.tsv | 1 + ...005_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...05_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-01_part-phase_events.tsv | 1 + ...5_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-005_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...05_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...005_task-mario3_run-02_part-mag_events.tsv | 1 + ...005_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...05_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-02_part-phase_events.tsv | 1 + ...5_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + sub-01/ses-005/sub-01_ses-005_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 51 files changed, 3485 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-005/anat/sub-01_ses-005_acq-axial_localizer.json create mode 120000 sub-01/ses-005/anat/sub-01_ses-005_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-005/anat/sub-01_ses-005_acq-coronal_localizer.json create mode 120000 sub-01/ses-005/anat/sub-01_ses-005_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-005/anat/sub-01_ses-005_acq-sagittal_localizer.json create mode 120000 sub-01/ses-005/anat/sub-01_ses-005_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-005/anat/sub-01_ses-005_scout.json create mode 120000 sub-01/ses-005/anat/sub-01_ses-005_scout.nii.gz create mode 100644 sub-01/ses-005/fmap/sub-01_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-005/fmap/sub-01_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-005/fmap/sub-01_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-005/fmap/sub-01_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-phase_sbref.nii.gz create mode 120000 sub-01/ses-005/sub-01_ses-005_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index bece9b3a0..e2e4a1ea3 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit bece9b3a08a756313ddc18e62e24d2d12c5df6cc +Subproject commit e2e4a1ea381f1981b3e5bb6d234998eda0f30253 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-005/anat/sub-01_ses-005_acq-axial_localizer.json b/sub-01/ses-005/anat/sub-01_ses-005_acq-axial_localizer.json new file mode 100644 index 000000000..141f609cb --- /dev/null +++ b/sub-01/ses-005/anat/sub-01_ses-005_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:41:24.035000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0351556, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 265.338 +} \ No newline at end of file diff --git a/sub-01/ses-005/anat/sub-01_ses-005_acq-axial_localizer.nii.gz b/sub-01/ses-005/anat/sub-01_ses-005_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..7bc0f3ec1 --- /dev/null +++ b/sub-01/ses-005/anat/sub-01_ses-005_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/WV/Z2/MD5E-s180013--95776378985c38cc05c26670aaa8c7e6.nii.gz/MD5E-s180013--95776378985c38cc05c26670aaa8c7e6.nii.gz \ No newline at end of file diff --git a/sub-01/ses-005/anat/sub-01_ses-005_acq-coronal_localizer.json b/sub-01/ses-005/anat/sub-01_ses-005_acq-coronal_localizer.json new file mode 100644 index 000000000..daa15d544 --- /dev/null +++ b/sub-01/ses-005/anat/sub-01_ses-005_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:41:31.025000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0351556, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 265.338 +} \ No newline at end of file diff --git a/sub-01/ses-005/anat/sub-01_ses-005_acq-coronal_localizer.nii.gz b/sub-01/ses-005/anat/sub-01_ses-005_acq-coronal_localizer.nii.gz new file mode 120000 index 000000000..0ebd27281 --- /dev/null +++ b/sub-01/ses-005/anat/sub-01_ses-005_acq-coronal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Pk/Q5/MD5E-s192655--3f90e10503ad81f734b7c8ec3c39735f.nii.gz/MD5E-s192655--3f90e10503ad81f734b7c8ec3c39735f.nii.gz \ No newline at end of file diff --git a/sub-01/ses-005/anat/sub-01_ses-005_acq-sagittal_localizer.json b/sub-01/ses-005/anat/sub-01_ses-005_acq-sagittal_localizer.json new file mode 100644 index 000000000..9d1b41ccb --- /dev/null +++ b/sub-01/ses-005/anat/sub-01_ses-005_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:41:17.045000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 0, + 1, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Sag", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": 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diff --git a/sub-01/ses-005/anat/sub-01_ses-005_scout.json b/sub-01/ses-005/anat/sub-01_ses-005_scout.json new file mode 100644 index 000000000..eeacca615 --- /dev/null +++ b/sub-01/ses-005/anat/sub-01_ses-005_scout.json @@ -0,0 +1,542 @@ +{ + "AcquisitionMatrixPE": 160, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:41:1.985000", + "BaseResolution": 160, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 5.8e-06, + "EchoTime": 0.00137, + "FlipAngle": 8, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [0, 1, 0, 0, 0, -1], + "ImageOrientationText": "Sag", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "ND", + "NORM" +], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "3D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "GRAPPA", + "Modality": "MR", + "ParallelReductionFactorInPlane": 3, + "PartialFourier": 0.75, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingSteps": 118, + "PhaseResolution": 1, + "PixelBandwidth": 540, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "AAHead_Scout", + "PulseSequenceDetails": "%SiemensSeq%\\AALScout", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 160, + "RefLinesPE": 24, + "RepetitionTime": 0.00315, + "SAR": 0.0240436, + "ScanOptions": "PFP", + "ScanningSequence": "GR", + "SequenceName": "*fl3d1_ns", + "SequenceVariant": "SP", + "SeriesDescription": "AAHead_Scout", + "SeriesNumber": 1, + 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b/sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-phase_bold.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/0F/Vf/MD5E-s386099979--5d64470accdf6248e63a1408c5d784df.nii.gz/MD5E-s386099979--5d64470accdf6248e63a1408c5d784df.nii.gz \ No newline at end of file diff --git a/sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-phase_events.tsv new file mode 120000 index 000000000..1bbdfddb5 --- /dev/null +++ b/sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-phase_events.tsv @@ -0,0 +1 @@ +../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-phase_sbref.json b/sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-phase_sbref.json new file mode 100644 index 000000000..908b63959 --- /dev/null +++ b/sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-phase_sbref.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:52:4.585000", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTime1": 0.037, + "EchoTime2": 0.001, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Single-band reference", + "ImageOrientationPatientDICOM": [ + 0.991201, + 0.130984, + 0.0190585, + -0.113809, + 0.9169, + -0.382547 + ], + "ImageOrientationText": "Tra>Cor(-22.2)>Sag(3.9)", + "ImageType": 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+../../.git/annex/objects/M6/5j/MD5E-s2045--4326f89cdffdb24024002152a58dff71.tsv/MD5E-s2045--4326f89cdffdb24024002152a58dff71.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..8175f3b2f --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": 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"ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0517807, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [627, -7194, -8835, 618, 103, -21, -64, 2], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 265.338, + "dcmmeta_affine": [ + [-1.9824026823043823, -0.22761887311935425, 0.1351640671491623, 112.38368225097656], + [-0.26196712255477905, 1.833799958229065, -0.7540232539176941, -43.454402923583984], + [0.03811696171760559, 0.7650931477546692, 1.847479224205017, -68.62422180175781], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 5a89471d1725179bb4dc1a2c665b61206ac9dd44 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:55:16 -0400 Subject: [PATCH 037/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-020_acq-axial_localizer.json | 81 +++ .../sub-01_ses-020_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-020_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-020_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-020_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-020_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-020/anat/sub-01_ses-020_scout.json | 542 ++++++++++++++++++ .../ses-020/anat/sub-01_ses-020_scout.nii.gz | 1 + ...0_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ...-020_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...20_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...020_task-mario3_run-01_part-mag_events.tsv | 1 + ...020_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...0_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...20_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...0_task-mario3_run-01_part-phase_events.tsv | 1 + ...0_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-020_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...20_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...020_task-mario3_run-02_part-mag_events.tsv | 1 + ...020_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...0_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...20_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...0_task-mario3_run-02_part-phase_events.tsv | 1 + ...0_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + sub-01/ses-020/sub-01_ses-020_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 51 files changed, 3485 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-020/anat/sub-01_ses-020_acq-axial_localizer.json create mode 120000 sub-01/ses-020/anat/sub-01_ses-020_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-020/anat/sub-01_ses-020_acq-coronal_localizer.json create mode 120000 sub-01/ses-020/anat/sub-01_ses-020_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-020/anat/sub-01_ses-020_acq-sagittal_localizer.json create mode 120000 sub-01/ses-020/anat/sub-01_ses-020_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-020/anat/sub-01_ses-020_scout.json create mode 120000 sub-01/ses-020/anat/sub-01_ses-020_scout.nii.gz create mode 100644 sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_sbref.nii.gz create mode 120000 sub-01/ses-020/sub-01_ses-020_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index f2b71fc6a..c7338348b 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit f2b71fc6a7fabff77091f4d0dd89e1f678cf29c4 +Subproject commit c7338348bf3d7d3ef84179abf2d8171890506061 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-020/anat/sub-01_ses-020_acq-axial_localizer.json b/sub-01/ses-020/anat/sub-01_ses-020_acq-axial_localizer.json new file mode 100644 index 000000000..c1b6ca792 --- /dev/null +++ b/sub-01/ses-020/anat/sub-01_ses-020_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:34:51.185000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": 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"N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.993693, 0.111268, 0.0138901, -0.0979578, 0.921684, -0.375371], + "ImageOrientationText": "Tra>Cor(-21.9)>Sag(3.1)", + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + 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112.1051025390625], + [-0.22253629565238953, 1.843367099761963, -0.7432868480682373, -46.462059020996094], + [0.027780262753367424, 0.7507427930831909, 1.8535408973693848, -60.74994659423828], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From e97136bf18c6b42e38598b81089ba0c5a017444f Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:55:17 -0400 Subject: [PATCH 038/463] fix fmap phase --- ...1_ses-005_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-005_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-005_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-005_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-005_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - sub-01/ses-005/sub-01_ses-005_scans.tsv | 2 +- 17 files changed, 1 insertion(+), 638 deletions(-) rename sub-01/ses-005/fmap/{sub-01_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-005_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-005/fmap/{sub-01_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-005_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-005/fmap/sub-01_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-005/fmap/sub-01_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-005/fmap/{sub-01_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-005_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-005/fmap/{sub-01_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-005_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-005/fmap/{sub-01_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-005_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-005/fmap/{sub-01_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-005_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-005/fmap/{sub-01_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-005_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-005/fmap/{sub-01_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-005_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz diff --git a/sub-01/ses-005/fmap/sub-01_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-005/fmap/sub-01_ses-005_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-005/fmap/sub-01_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-005/fmap/sub-01_ses-005_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-005/fmap/sub-01_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-005/fmap/sub-01_ses-005_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-005/fmap/sub-01_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-005/fmap/sub-01_ses-005_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-005/fmap/sub-01_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-005/fmap/sub-01_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index caf78bae4..000000000 --- a/sub-01/ses-005/fmap/sub-01_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:42:26.717500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": 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-../../../.git/annex/objects/QM/mQ/MD5E-s3334844--dac3bc7c3eb953df4a35073b7d64f171.nii.gz/MD5E-s3334844--dac3bc7c3eb953df4a35073b7d64f171.nii.gz \ No newline at end of file diff --git a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 9eedad27a..000000000 --- a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:42:16.287500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.991201, - 0.130984, - 0.0190585, - -0.113809, - 0.9169, - -0.382547 - ], - "ImageOrientationText": "Tra>Cor(-22.2)>Sag(3.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0412953, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 627, - -7194, - -8835, - 618, - 103, - -21, - -64, - 2 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 265.338, - "WipMemBlock": "54268fd1-7246-4e35-92bb-c584ec4fefc5||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 0aeae731f..000000000 --- a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/zj/gx/MD5E-s1112386--7d3854594f1e49c829c86ef5565eced6.nii.gz/MD5E-s1112386--7d3854594f1e49c829c86ef5565eced6.nii.gz \ No newline at end of file diff --git a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 9423b9585..000000000 --- a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:42:58.425000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.991201, - 0.130984, - 0.0190585, - -0.113809, - 0.9169, - -0.382547 - ], - "ImageOrientationText": "Tra>Cor(-22.2)>Sag(3.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0517807, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 627, - -7194, - -8835, - 618, - 103, - -21, - -64, - 2 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 265.338, - "WipMemBlock": "702ec4ab-cfe0-452e-976b-03a454793a64||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 729677fd5..000000000 --- a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/vk/wk/MD5E-s1103789--88e3938b8d003c48bef8eff4dbf65840.nii.gz/MD5E-s1103789--88e3938b8d003c48bef8eff4dbf65840.nii.gz \ No newline at end of file diff --git a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 5f1ad368d..000000000 --- a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:52:4.585000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.991201, - 0.130984, - 0.0190585, - -0.113809, - 0.9169, - -0.382547 - ], - "ImageOrientationText": "Tra>Cor(-22.2)>Sag(3.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0517807, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 627, - -7194, - -8835, - 618, - 103, - -21, - -64, - 2 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 265.338, - "WipMemBlock": "f20e336c-35af-4173-b792-f93e50c55891||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 34c55571e..000000000 --- a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Xp/p8/MD5E-s1103966--4154f16ed744876fb0e2d13108557bce.nii.gz/MD5E-s1103966--4154f16ed744876fb0e2d13108557bce.nii.gz \ No newline at end of file diff --git a/sub-01/ses-005/sub-01_ses-005_scans.tsv b/sub-01/ses-005/sub-01_ses-005_scans.tsv index 829bac0b1..d14738a9a 120000 --- a/sub-01/ses-005/sub-01_ses-005_scans.tsv +++ b/sub-01/ses-005/sub-01_ses-005_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/M6/5j/MD5E-s2045--4326f89cdffdb24024002152a58dff71.tsv/MD5E-s2045--4326f89cdffdb24024002152a58dff71.tsv \ No newline at end of file +../../.git/annex/objects/Z0/1x/MD5E-s1565--98d21278b4862221a4f009c0fbd7f2f1.tsv/MD5E-s1565--98d21278b4862221a4f009c0fbd7f2f1.tsv \ No newline at end of file From c16de7fc6dd9810e359bc846818f706c8325e2a7 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:55:27 -0400 Subject: [PATCH 039/463] fix complex event files --- ...g_events.tsv => sub-01_ses-005_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-005_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-005_task-mario3_run-02_part-mag_events.tsv | 1 - .../func/sub-01_ses-005_task-mario3_run-02_part-phase_events.tsv | 1 - 4 files changed, 2 deletions(-) rename sub-01/ses-005/func/{sub-01_ses-005_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-005_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-005/func/{sub-01_ses-005_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-005_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-mag_events.tsv delete mode 120000 sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-phase_events.tsv diff --git a/sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-005/func/sub-01_ses-005_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 020759f360f7aa360f4ffc3a51404cae612c00c8 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:55:57 -0400 Subject: [PATCH 040/463] fix fmap phase --- ...1_ses-020_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-020_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-020_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-020_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-020_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-020_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-020_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-020_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - sub-01/ses-020/sub-01_ses-020_scans.tsv | 2 +- 17 files changed, 1 insertion(+), 638 deletions(-) rename sub-01/ses-020/fmap/{sub-01_ses-020_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-020_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-020/fmap/{sub-01_ses-020_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-020_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-020/fmap/{sub-01_ses-020_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-020_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-020/fmap/{sub-01_ses-020_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-020_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-020/fmap/{sub-01_ses-020_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-020_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-020/fmap/{sub-01_ses-020_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-020_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-020/fmap/{sub-01_ses-020_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-020_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-020/fmap/{sub-01_ses-020_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-020_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index c79df6cfa..000000000 --- a/sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:35:51.325000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.993693, 0.111268, 0.0138901, -0.0979578, 0.921684, -0.375371], - "ImageOrientationText": "Tra>Cor(-21.9)>Sag(3.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - 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0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 270.989, - "WipMemBlock": "3200bd58-69df-4178-92a7-ad1d9be22510||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.987386703491211, -0.19591569900512695, 0.1091383695602417, 112.1051025390625], - [-0.22253629565238953, 1.843367099761963, -0.7432868480682373, -46.462059020996094], - [0.027780262753367424, 0.7507427930831909, 1.8535408973693848, -60.74994659423828], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99369334521862, 0.11126814424251, 0.01389013121101, -0.0979578467932, 0.92168355269881, -0.3753714013296], - "ImagePositionPatient": [-744.02122954796, -895.39358742891, 279.73492825906], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.260196, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "113403.789000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.04339672857139, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "113638.348000", - "SliceLocation": -32.916448212228, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000661501, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "113403.709000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["113551.325000", "113552.815000", "113554.305000"], - "ContentTime": ["113638.350000", "113638.352000", "113638.364000"], - "InstanceCreationTime": ["113638.350000", "113638.352000", "113638.364000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4796.0, 4800.0, 4796.0], - "WindowWidth": [18552.0, 18554.0, 18558.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 58ac26f48..000000000 --- a/sub-01/ses-020/fmap/sub-01_ses-020_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/g0/pK/MD5E-s3335391--072210bc86f0c27fd8a18d65ee876b1a.nii.gz/MD5E-s3335391--072210bc86f0c27fd8a18d65ee876b1a.nii.gz \ No newline at end of file diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index c9958eb7d..000000000 --- a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:35:40.895000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993693, - 0.111268, - 0.0138901, - -0.0979578, - 0.921684, - -0.375371 - ], - "ImageOrientationText": "Tra>Cor(-21.9)>Sag(3.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0433967, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 611, - -7189, - -8819, - 623, - 78, - 15, - -92, - 3 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 270.989, - "WipMemBlock": "3200bd58-69df-4178-92a7-ad1d9be22510||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index a3adc7e10..000000000 --- a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/p8/mQ/MD5E-s1112263--a5a7426207955f40d5ae0d00a9d9cbc9.nii.gz/MD5E-s1112263--a5a7426207955f40d5ae0d00a9d9cbc9.nii.gz \ No newline at end of file diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 56a64d811..000000000 --- a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:38:8.257500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993693, - 0.111268, - 0.0138901, - -0.0979578, - 0.921684, - -0.375371 - ], - "ImageOrientationText": "Tra>Cor(-21.9)>Sag(3.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0544157, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 611, - -7189, - -8819, - 623, - 78, - 15, - -92, - 3 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 270.989, - "WipMemBlock": "412b1ffc-43d4-487a-9cf3-7a99f5d61c73||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 20ec42a16..000000000 --- a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Mq/Fj/MD5E-s1103752--41e537e860cd931f356fb1ddf5aec096.nii.gz/MD5E-s1103752--41e537e860cd931f356fb1ddf5aec096.nii.gz \ No newline at end of file diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 18560f787..000000000 --- a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:55:35.152500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993693, - 0.111268, - 0.0138901, - -0.0979578, - 0.921684, - -0.375371 - ], - "ImageOrientationText": "Tra>Cor(-21.9)>Sag(3.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0544157, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 611, - -7189, - -8819, - 623, - 78, - 15, - -92, - 3 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 270.989, - "WipMemBlock": "c502df24-9bc1-43ec-932b-ca49bfae725c||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 255f8fd1f..000000000 --- a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/8F/z7/MD5E-s1103842--6cff3d1ff62ef85562aeb9cbceb610f3.nii.gz/MD5E-s1103842--6cff3d1ff62ef85562aeb9cbceb610f3.nii.gz \ No newline at end of file diff --git a/sub-01/ses-020/sub-01_ses-020_scans.tsv b/sub-01/ses-020/sub-01_ses-020_scans.tsv index 1cea63f27..038bfa8bb 120000 --- a/sub-01/ses-020/sub-01_ses-020_scans.tsv +++ b/sub-01/ses-020/sub-01_ses-020_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/5p/P7/MD5E-s2045--04a26a465e96e5c69650a4e729cee744.tsv/MD5E-s2045--04a26a465e96e5c69650a4e729cee744.tsv \ No newline at end of file +../../.git/annex/objects/1K/46/MD5E-s1565--3a489f74f260fbf5206c05cf8eb7487e.tsv/MD5E-s1565--3a489f74f260fbf5206c05cf8eb7487e.tsv \ No newline at end of file From b6e9b2f472aef41767e3314fe0f3b20fecf7647e Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:56:07 -0400 Subject: [PATCH 041/463] fix complex event files --- ...g_events.tsv => sub-01_ses-020_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-020_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-020_task-mario3_run-02_part-mag_events.tsv | 1 - .../func/sub-01_ses-020_task-mario3_run-02_part-phase_events.tsv | 1 - 4 files changed, 2 deletions(-) rename sub-01/ses-020/func/{sub-01_ses-020_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-020_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-020/func/{sub-01_ses-020_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-020_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_events.tsv delete mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_events.tsv diff --git a/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From eea74c4749462afa659fb959766a96879380a8c3 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:56:38 -0400 Subject: [PATCH 042/463] fill IntendedFor --- ...1_ses-005_acq-sbref_dir-AP_run-01_epi.json | 89 ++----------------- ...1_ses-005_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-005_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- 3 files changed, 22 insertions(+), 243 deletions(-) diff --git a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_epi.json index 06cf20285..dc8ffcdd1 100644 --- a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.991201, - 0.130984, - 0.0190585, - -0.113809, - 0.9169, - -0.382547 - ], + "ImageOrientationPatientDICOM": [0.991201, 0.130984, 0.0190585, -0.113809, 0.9169, -0.382547], "ImageOrientationText": "Tra>Cor(-22.2)>Sag(3.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,16 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-01_ses-005_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-005/func/sub-01_ses-005_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +64,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 627, - -7194, - -8835, - 618, - 103, - -21, - -64, - 2 - ], + "ShimSetting": [627, -7194, -8835, 618, 103, -21, -64, 2], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_epi.json index ff1561b7c..5b34aafc5 100644 --- a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.991201, - 0.130984, - 0.0190585, - -0.113809, - 0.9169, - -0.382547 - ], + "ImageOrientationPatientDICOM": [0.991201, 0.130984, 0.0190585, -0.113809, 0.9169, -0.382547], "ImageOrientationText": "Tra>Cor(-22.2)>Sag(3.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-01_ses-005_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 627, - -7194, - -8835, - 618, - 103, - -21, - -64, - 2 - ], + "ShimSetting": [627, -7194, -8835, 618, 103, -21, -64, 2], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_epi.json index 2efd26e71..bf0bbb897 100644 --- a/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-005/fmap/sub-01_ses-005_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.991201, - 0.130984, - 0.0190585, - -0.113809, - 0.9169, - -0.382547 - ], + "ImageOrientationPatientDICOM": [0.991201, 0.130984, 0.0190585, -0.113809, 0.9169, -0.382547], "ImageOrientationText": "Tra>Cor(-22.2)>Sag(3.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-01_ses-005_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 627, - -7194, - -8835, - 618, - 103, - -21, - -64, - 2 - ], + "ShimSetting": [627, -7194, -8835, 618, 103, -21, -64, 2], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From b5ab2016cb8f727df98cfad284272f7421feb41a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:57:12 -0400 Subject: [PATCH 043/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..0e691c46f --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = f19c3519-5bec-41fe-bc09-f4ebde4611c5 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..3a3bcf3af --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 3a3bcf3af9171967ae08f17df26248a048e39f51 From 4cc9edf48df2c712184610da36588c6c6219e58a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:57:19 -0400 Subject: [PATCH 044/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..b0d6c227a --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = c4230de8-5e42-432e-8e22-8a3e4bdaf6da diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..1f5350ce4 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 1f5350ce4a27e209616a162a2d3859ec55310ea8 From 54c959b94d49b018524f8b469a721fe951b05368 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:57:23 -0400 Subject: [PATCH 045/463] fill IntendedFor --- ...1_ses-020_acq-sbref_dir-AP_run-01_epi.json | 89 ++----------------- ...1_ses-020_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-020_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- 3 files changed, 22 insertions(+), 243 deletions(-) diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_epi.json index 5f790fc3f..5a5f3a34a 100644 --- a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993693, - 0.111268, - 0.0138901, - -0.0979578, - 0.921684, - -0.375371 - ], + "ImageOrientationPatientDICOM": [0.993693, 0.111268, 0.0138901, -0.0979578, 0.921684, -0.375371], "ImageOrientationText": "Tra>Cor(-21.9)>Sag(3.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,16 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-020/func/sub-01_ses-020_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +64,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 611, - -7189, - -8819, - 623, - 78, - 15, - -92, - 3 - ], + "ShimSetting": [611, -7189, -8819, 623, 78, 15, -92, 3], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_epi.json index a49026972..30a443f36 100644 --- a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993693, - 0.111268, - 0.0138901, - -0.0979578, - 0.921684, - -0.375371 - ], + "ImageOrientationPatientDICOM": [0.993693, 0.111268, 0.0138901, -0.0979578, 0.921684, -0.375371], "ImageOrientationText": "Tra>Cor(-21.9)>Sag(3.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-020/func/sub-01_ses-020_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 611, - -7189, - -8819, - 623, - 78, - 15, - -92, - 3 - ], + "ShimSetting": [611, -7189, -8819, 623, 78, 15, -92, 3], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_epi.json index 9abae464c..45706ef82 100644 --- a/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-020/fmap/sub-01_ses-020_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993693, - 0.111268, - 0.0138901, - -0.0979578, - 0.921684, - -0.375371 - ], + "ImageOrientationPatientDICOM": [0.993693, 0.111268, 0.0138901, -0.0979578, 0.921684, -0.375371], "ImageOrientationText": "Tra>Cor(-21.9)>Sag(3.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 611, - -7189, - -8819, - 623, - 78, - 15, - -92, - 3 - ], + "ShimSetting": [611, -7189, -8819, 623, 78, 15, -92, 3], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 77e47b1870febe40524a5dac81062a84e3117655 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:57:26 -0400 Subject: [PATCH 046/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..4e69bce2d --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = d97968be-0967-49c6-a766-2f71f3799dfa diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..f5c13dab4 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit f5c13dab41de8c7a7c801aacf9308c60d4531af7 From e80eef0d396d40262abf054dae6c9a0f6063ecd8 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:57:38 -0400 Subject: [PATCH 047/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..b51957038 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 5f14afdc-ef6f-4eae-85c2-ec34e03bee18 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..21a92023e --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 21a92023ed800343fac1176a93a829c8a8e8933d From 02b7452ce825d8d5bf8043a8602a73d7fbf0aeff Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:57:49 -0400 Subject: [PATCH 048/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-008_acq-axial_localizer.json | 81 +++ .../sub-01_ses-008_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-008_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-008_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-008_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-008_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-008/anat/sub-01_ses-008_scout.json | 542 ++++++++++++++++++ .../ses-008/anat/sub-01_ses-008_scout.nii.gz | 1 + ...8_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + .../func/sub-01_ses-008_part-mag_bold.json | 171 ++++++ .../func/sub-01_ses-008_part-mag_bold.nii.gz | 1 + .../func/sub-01_ses-008_part-mag_sbref.json | 149 +++++ .../func/sub-01_ses-008_part-mag_sbref.nii.gz | 1 + .../func/sub-01_ses-008_part-phase_bold.json | 177 ++++++ .../sub-01_ses-008_part-phase_bold.nii.gz | 1 + .../func/sub-01_ses-008_part-phase_sbref.json | 152 +++++ .../sub-01_ses-008_part-phase_sbref.nii.gz | 1 + ...-008_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-01_part-mag_events.tsv | 1 + ...008_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-01_part-phase_events.tsv | 1 + ...8_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-008_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-02_part-mag_events.tsv | 1 + ...008_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-02_part-phase_events.tsv | 1 + ...8_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + sub-01/ses-008/sub-01_ses-008_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 63 files changed, 4441 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-008/anat/sub-01_ses-008_acq-axial_localizer.json create mode 120000 sub-01/ses-008/anat/sub-01_ses-008_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-008/anat/sub-01_ses-008_acq-coronal_localizer.json create mode 120000 sub-01/ses-008/anat/sub-01_ses-008_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-008/anat/sub-01_ses-008_acq-sagittal_localizer.json create mode 120000 sub-01/ses-008/anat/sub-01_ses-008_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-008/anat/sub-01_ses-008_scout.json create mode 120000 sub-01/ses-008/anat/sub-01_ses-008_scout.nii.gz create mode 100644 sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-01/ses-008/func/sub-01_ses-008_part-mag_bold.json create mode 120000 sub-01/ses-008/func/sub-01_ses-008_part-mag_bold.nii.gz create mode 100644 sub-01/ses-008/func/sub-01_ses-008_part-mag_sbref.json create mode 120000 sub-01/ses-008/func/sub-01_ses-008_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-008/func/sub-01_ses-008_part-phase_bold.json create mode 120000 sub-01/ses-008/func/sub-01_ses-008_part-phase_bold.nii.gz create mode 100644 sub-01/ses-008/func/sub-01_ses-008_part-phase_sbref.json create mode 120000 sub-01/ses-008/func/sub-01_ses-008_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_part-phase_sbref.nii.gz create mode 120000 sub-01/ses-008/sub-01_ses-008_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 3a3bcf3af..bfac2a817 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 3a3bcf3af9171967ae08f17df26248a048e39f51 +Subproject commit bfac2a817de506acdda46fa8bed4de3a41eab142 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-008/anat/sub-01_ses-008_acq-axial_localizer.json b/sub-01/ses-008/anat/sub-01_ses-008_acq-axial_localizer.json new file mode 100644 index 000000000..a7d6f8498 --- /dev/null +++ b/sub-01/ses-008/anat/sub-01_ses-008_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:45:35.067500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0352643, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 259.777 +} \ No newline at end of file diff --git a/sub-01/ses-008/anat/sub-01_ses-008_acq-axial_localizer.nii.gz b/sub-01/ses-008/anat/sub-01_ses-008_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..1930f3cbf --- /dev/null +++ b/sub-01/ses-008/anat/sub-01_ses-008_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Pj/8j/MD5E-s178594--04c96cc0e42a7a17b143696774da0018.nii.gz/MD5E-s178594--04c96cc0e42a7a17b143696774da0018.nii.gz \ No newline at end of file diff --git a/sub-01/ses-008/anat/sub-01_ses-008_acq-coronal_localizer.json b/sub-01/ses-008/anat/sub-01_ses-008_acq-coronal_localizer.json new file mode 100644 index 000000000..719de7f6c --- /dev/null +++ b/sub-01/ses-008/anat/sub-01_ses-008_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:45:42.057500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0352643, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 259.777 +} \ No newline at end of file diff --git a/sub-01/ses-008/anat/sub-01_ses-008_acq-coronal_localizer.nii.gz b/sub-01/ses-008/anat/sub-01_ses-008_acq-coronal_localizer.nii.gz new file mode 120000 index 000000000..5966d1f29 --- /dev/null +++ b/sub-01/ses-008/anat/sub-01_ses-008_acq-coronal_localizer.nii.gz @@ -0,0 +1 @@ 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"ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0519409, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [631, -7197, -8760, 668, 69, 15, 11, 0], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 259.777, + "dcmmeta_affine": [ + [-1.9900315999984741, -0.15452224016189575, 0.12608401477336884, 110.4366455078125], + [-0.18580162525177002, 1.8959392309188843, -0.6090090870857239, -52.87593460083008], + [0.07247108966112137, 0.617686927318573, 1.9008448123931885, -47.507083892822266], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 5e4eabcec24b17ba60d7ca359c40dabfeae89e0f Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:58:50 -0400 Subject: [PATCH 049/463] fix fmap phase --- ...1_ses-008_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-008_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-008_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-01/ses-008/sub-01_ses-008_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-01/ses-008/fmap/{sub-01_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-008_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-008/fmap/{sub-01_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-008_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-008/fmap/{sub-01_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-008_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-008/fmap/{sub-01_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-008_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-008/fmap/{sub-01_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-008_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-008/fmap/{sub-01_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-008_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-008/fmap/{sub-01_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-008_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-008/fmap/{sub-01_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-008_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-01/ses-008/fmap/{sub-01_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-01_ses-008_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-01/ses-008/fmap/{sub-01_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-01_ses-008_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 7399b01d7..000000000 --- a/sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:51:15.085000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.995016, 0.0929008, 0.0362355, -0.0772611, 0.94797, -0.308843], - "ImageOrientationText": "Tra>Cor(-17.8)>Sag(3.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - 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0.12608401477336884, 110.4366455078125], - [-0.18580162525177002, 1.8959392309188843, -0.6090090870857239, -59.06544876098633], - [0.07247108966112137, 0.617686927318573, 1.9008448123931885, -47.507083892822266], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99501579092909, 0.09290081267399, 0.03623554617055, -0.0772611227571, 0.9479696328722, -0.308843478258], - "ImagePositionPatient": [-762.64625454175, -893.96997950852, 214.57324821193], - "ImageType": [ - "ORIGINAL", - 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"SeriesDescription": "func_AP_run-1", - "SeriesNumber": 11, - "SeriesTime": "185201.966000", - "SliceLocation": -20.203949204788, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000547342, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "184432.898000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["185115.085000", "185116.575000", "185118.065000"], - "ContentTime": ["185201.968000", "185201.971000", "185201.973000"], - "InstanceCreationTime": ["185201.968000", "185201.971000", "185201.973000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4854.0, 4854.0, 4852.0], - "WindowWidth": [18634.0, 18632.0, 18636.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index d8aa0ecb4..000000000 --- a/sub-01/ses-008/fmap/sub-01_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/jV/KF/MD5E-s3335303--462bcc998a0db0b305fa9a042e63f3c5.nii.gz/MD5E-s3335303--462bcc998a0db0b305fa9a042e63f3c5.nii.gz \ No newline at end of file diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 2f7ca2387..000000000 --- a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:51:4.655000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - 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a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/m4/G9/MD5E-s1112431--5407ae0d4574cc711e352584c61c0f76.nii.gz/MD5E-s1112431--5407ae0d4574cc711e352584c61c0f76.nii.gz \ No newline at end of file diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 9c88353f6..000000000 --- a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:47:59.230000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": 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"ProtocolName": "func_test", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0519409, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_test_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 635, - -7196, - -8753, - 689, - 82, - 7, - 19, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 259.777, - "WipMemBlock": "2b866f2a-08ca-4c1e-8745-c2aa8dd3ed87||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 70976d43a..000000000 --- a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/XX/82/MD5E-s1103826--36376e0fdad0cb0e22a410ba88e4a989.nii.gz/MD5E-s1103826--36376e0fdad0cb0e22a410ba88e4a989.nii.gz \ No newline at end of file diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 036480350..000000000 --- a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:52:44.257500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995016, - 0.0929008, - 0.0362355, - -0.0772611, - 0.94797, - -0.308843 - ], - "ImageOrientationText": "Tra>Cor(-17.8)>Sag(3.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0519409, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 631, - -7197, - -8760, - 668, - 69, - 15, - 11, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.51, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 259.777, - "WipMemBlock": "057e5558-cec4-4ec6-9b00-d5d4e4a51b73||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 975377462..000000000 --- a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/G2/V6/MD5E-s1103847--1e2643c3d39b9cfe7d6f5a617cac2746.nii.gz/MD5E-s1103847--1e2643c3d39b9cfe7d6f5a617cac2746.nii.gz \ No newline at end of file diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 0f7bd6fb2..000000000 --- a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:03:33.572500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995016, - 0.0929008, - 0.0362355, - -0.0772611, - 0.94797, - -0.308843 - ], - "ImageOrientationText": "Tra>Cor(-17.8)>Sag(3.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0519409, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 631, - -7197, - -8760, - 668, - 69, - 15, - 11, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 259.777, - "WipMemBlock": "efb53e34-432d-4d83-9f38-eea1092e1d8b||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index b039e3b43..000000000 --- a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Qk/3g/MD5E-s1103991--7b0b95055a2274a45af101cb9a10afe5.nii.gz/MD5E-s1103991--7b0b95055a2274a45af101cb9a10afe5.nii.gz \ No newline at end of file diff --git a/sub-01/ses-008/sub-01_ses-008_scans.tsv b/sub-01/ses-008/sub-01_ses-008_scans.tsv index 73ca7c4c0..3ca318b1b 120000 --- a/sub-01/ses-008/sub-01_ses-008_scans.tsv +++ b/sub-01/ses-008/sub-01_ses-008_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/3F/Zj/MD5E-s2584--17965c1eab66d4cceb3a75205854733b.tsv/MD5E-s2584--17965c1eab66d4cceb3a75205854733b.tsv \ No newline at end of file +../../.git/annex/objects/M1/xk/MD5E-s1983--c53896f6f7b56323dec9dcbde3fe28d4.tsv/MD5E-s1983--c53896f6f7b56323dec9dcbde3fe28d4.tsv \ No newline at end of file From 50f9a88c1bf135e6a476e7508052d0728464f136 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:58:59 -0400 Subject: [PATCH 050/463] fix complex event files --- ...g_events.tsv => sub-01_ses-008_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-008_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-008_task-mario3_run-02_part-mag_events.tsv | 1 - .../func/sub-01_ses-008_task-mario3_run-02_part-phase_events.tsv | 1 - 4 files changed, 2 deletions(-) rename sub-01/ses-008/func/{sub-01_ses-008_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-008_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-008/func/{sub-01_ses-008_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-008_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_part-mag_events.tsv delete mode 120000 sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_part-phase_events.tsv diff --git a/sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-008/func/sub-01_ses-008_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 2e3adad363459550d4ef310c63a5fc67137ced03 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:59:06 -0400 Subject: [PATCH 051/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..8f35b3c06 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 3a96c185-e877-4ad1-ac6f-2c0e76a46893 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..0bfae1038 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 0bfae103818e285a772dc5335d589ac6efc9d6d4 From d5c087ec57c18ccb2b876044dd9d94d9cc3a2d14 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 14:59:07 -0400 Subject: [PATCH 052/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-002_acq-axial_localizer.json | 81 +++ .../sub-01_ses-002_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-002_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-002_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-002_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-002_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-002/anat/sub-01_ses-002_scout.json | 542 ++++++++++++++++++ .../ses-002/anat/sub-01_ses-002_scout.nii.gz | 1 + ...2_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-002_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-01_part-mag_events.tsv | 1 + ...002_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-01_part-phase_events.tsv | 1 + ...2_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-002_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-02_part-mag_events.tsv | 1 + ...002_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-02_part-phase_events.tsv | 1 + ...2_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-002_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-03_part-mag_events.tsv | 1 + ...002_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-03_part-phase_events.tsv | 1 + ...2_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-01/ses-002/sub-01_ses-002_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-002/anat/sub-01_ses-002_acq-axial_localizer.json create mode 120000 sub-01/ses-002/anat/sub-01_ses-002_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-002/anat/sub-01_ses-002_acq-coronal_localizer.json create mode 120000 sub-01/ses-002/anat/sub-01_ses-002_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-002/anat/sub-01_ses-002_acq-sagittal_localizer.json create mode 120000 sub-01/ses-002/anat/sub-01_ses-002_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-002/anat/sub-01_ses-002_scout.json create mode 120000 sub-01/ses-002/anat/sub-01_ses-002_scout.nii.gz create mode 100644 sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-01/ses-002/sub-01_ses-002_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 1f5350ce4..d953911a8 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 1f5350ce4a27e209616a162a2d3859ec55310ea8 +Subproject commit d953911a8abf29a974fa701b47dc830664e71e54 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-002/anat/sub-01_ses-002_acq-axial_localizer.json b/sub-01/ses-002/anat/sub-01_ses-002_acq-axial_localizer.json new file mode 100644 index 000000000..1808eebf2 --- /dev/null +++ b/sub-01/ses-002/anat/sub-01_ses-002_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:41:33.052500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0311903, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 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+../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-phase_sbref.json b/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-phase_sbref.json new file mode 100644 index 000000000..5ecbc6002 --- /dev/null +++ b/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-phase_sbref.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "19:02:12.715000", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + 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2.8425, + 2.94, + 3.0375, + 3.135, + 3.235, + 3.3325, + 3.43, + 3.5275, + 3.625, + 3.725, + 3.8225, + 3.92, + 4.0175, + 4.115, + 4.215, + 4.3125, + 4.41, + 4.5075, + 4.605, + 4.705, + 4.8025, + 4.9, + 4.9975, + 5.095, + 5.195, + 5.2925, + 5.39, + 5.4875, + 5.585, + 5.685, + 5.7825 + ], + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 249.116, + "WipMemBlock": "c35b16e6-6e9e-4aa0-806e-1b4c3abe0ff2||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-phase_sbref.nii.gz b/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-phase_sbref.nii.gz new file mode 120000 index 000000000..556df352f --- /dev/null +++ b/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Q3/5k/MD5E-s1103846--240325d639e7fa727ab20dd00383ce4e.nii.gz/MD5E-s1103846--240325d639e7fa727ab20dd00383ce4e.nii.gz \ No newline at end of file diff --git a/sub-01/ses-002/sub-01_ses-002_scans.tsv b/sub-01/ses-002/sub-01_ses-002_scans.tsv new file mode 120000 index 000000000..2a60a6b48 --- /dev/null +++ b/sub-01/ses-002/sub-01_ses-002_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/Mw/Kf/MD5E-s2667--8762ea3056e44332395a4e15b2fc1611.tsv/MD5E-s2667--8762ea3056e44332395a4e15b2fc1611.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..866834e53 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.997011, 0.0768685, 0.00781709, -0.0690184, 0.931508, -0.357112], + "ImageOrientationText": "Tra>Cor(-20.8)>Sag(2.0)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0459403, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [622, -7194, -8810, 631, 81, 16, -45, -5], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 249.116, + "dcmmeta_affine": [ + [-1.9940211772918701, -0.13803672790527344, 0.06946469843387604, 110.95624542236328], + [-0.15373696386814117, 1.8630162477493286, -0.7110100388526917, -52.16655349731445], + [0.01563418097794056, 0.7142242193222046, 1.8680577278137207, -59.22541427612305], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From d617dbcf2ddbb6dbb0ea161ab7d16b8ed3d187bf Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:00:11 -0400 Subject: [PATCH 053/463] fill IntendedFor --- ...1_ses-008_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...1_ses-008_acq-sbref_dir-PA_run-01_epi.json | 90 ++----------------- 2 files changed, 18 insertions(+), 162 deletions(-) diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_epi.json index 2607dcc38..de5f8cab4 100644 --- a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995016, - 0.0929008, - 0.0362355, - -0.0772611, - 0.94797, - -0.308843 - ], + "ImageOrientationPatientDICOM": [0.995016, 0.0929008, 0.0362355, -0.0772611, 0.94797, -0.308843], "ImageOrientationText": "Tra>Cor(-17.8)>Sag(3.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-01_ses-008_part-mag_bold.nii.gz", + "ses-008/func/sub-01_ses-008_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-008/func/sub-01_ses-008_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 635, - -7196, - -8753, - 689, - 82, - 7, - 19, - 0 - ], + "ShimSetting": [635, -7196, -8753, 689, 82, 7, 19, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_epi.json index b858eeb3f..ad68b30d4 100644 --- a/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-008/fmap/sub-01_ses-008_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995016, - 0.0929008, - 0.0362355, - -0.0772611, - 0.94797, - -0.308843 - ], + "ImageOrientationPatientDICOM": [0.995016, 0.0929008, 0.0362355, -0.0772611, 0.94797, -0.308843], "ImageOrientationText": "Tra>Cor(-17.8)>Sag(3.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-01_ses-008_part-mag_bold.nii.gz", + "ses-008/func/sub-01_ses-008_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-008/func/sub-01_ses-008_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_test_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 635, - -7196, - -8753, - 689, - 82, - 7, - 19, - 0 - ], + "ShimSetting": [635, -7196, -8753, 689, 82, 7, 19, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 5197a8500e42b6df10eaffb6141cb9ed3e455612 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:00:18 -0400 Subject: [PATCH 054/463] fix fmap phase --- ...1_ses-002_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-002_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-002_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-01/ses-002/sub-01_ses-002_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-01/ses-002/fmap/{sub-01_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-002_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-002/fmap/{sub-01_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-002_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-002/fmap/{sub-01_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-002_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-002/fmap/{sub-01_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-002_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-002/fmap/{sub-01_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-002_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-002/fmap/{sub-01_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-002_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-002/fmap/{sub-01_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-002_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-002/fmap/{sub-01_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-002_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-01/ses-002/fmap/{sub-01_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-01_ses-002_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-01/ses-002/fmap/{sub-01_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-01_ses-002_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index fa418ee60..000000000 --- a/sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:42:45.702500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.997011, 0.0768685, 0.00781709, -0.0690184, 0.931508, -0.357112], - "ImageOrientationText": "Tra>Cor(-20.8)>Sag(2.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0366375, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [622, -7194, -8810, 631, 81, 16, -45, -5], - "SliceThickness": 2, - "SliceTiming": [0, 0.7825, 0.0975, 0.88, 0.195, 0.98, 0.2925, 1.0775, 0.39, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685, 0, 0.7825, 0.0975, 0.88, 0.195, 0.98, 0.2925, 1.0775, 0.39, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685, 0, 0.7825, 0.0975, 0.88, 0.195, 0.98, 0.2925, 1.0775, 0.39, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685, 0, 0.7825, 0.0975, 0.88, 0.195, 0.98, 0.2925, 1.0775, 0.39, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 249.116, - "WipMemBlock": "5cfce54c-b076-43a6-8f10-e4122958f2c9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9940211772918701, -0.13803672790527344, 0.06946469843387604, 110.95624542236328], - [-0.15373696386814117, 1.8630162477493286, -0.7110100388526917, -52.16655349731445], - [0.01563418097794056, 0.7142242193222046, 1.8680577278137207, -59.22541427612305], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99701059643775, 0.07686848300886, 0.00781709093924, -0.0690183637188, 0.93150814092855, -0.3571120956414], - "ImagePositionPatient": [-772.31680813593, -873.82230598042, 268.6264405858], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.258804, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "184017.187000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.03663754976905, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "184332.310000", - "SliceLocation": -32.919001662154, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000381298, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "184017.114000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["184245.702500", "184247.192500", "184248.682500"], - "ContentTime": ["184332.312000", "184332.315000", "184332.318000"], - "InstanceCreationTime": ["184332.312000", "184332.315000", "184332.318000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4828.0, 4822.0, 4824.0], - "WindowWidth": [18570.0, 18570.0, 18568.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 421fdc42a..000000000 --- a/sub-01/ses-002/fmap/sub-01_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/mp/68/MD5E-s3335070--b4f423d78649cf6c6d5ee55830ef384d.nii.gz/MD5E-s3335070--b4f423d78649cf6c6d5ee55830ef384d.nii.gz \ No newline at end of file diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 33664b582..000000000 --- a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:42:35.272500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997011, - 0.0768685, - 0.00781709, - -0.0690184, - 0.931508, - -0.357112 - ], - "ImageOrientationText": "Tra>Cor(-20.8)>Sag(2.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0366375, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 622, - -7194, - -8810, - 631, - 81, - 16, - -45, - -5 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 249.116, - "WipMemBlock": "5cfce54c-b076-43a6-8f10-e4122958f2c9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 6209a3426..000000000 --- a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Xx/kw/MD5E-s1112213--59c53a174b926eb4099e95c297e2d7f4.nii.gz/MD5E-s1112213--59c53a174b926eb4099e95c297e2d7f4.nii.gz \ No newline at end of file diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 0432d2756..000000000 --- a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:44:12.127500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997011, - 0.0768685, - 0.00781709, - -0.0690184, - 0.931508, - -0.357112 - ], - "ImageOrientationText": "Tra>Cor(-20.8)>Sag(2.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0459403, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 622, - -7194, - -8810, - 631, - 81, - 16, - -45, - -5 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 249.116, - "WipMemBlock": "dbd58dcf-d11d-4b1e-b3b1-2c15ffb3cb73||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index bc2e464ab..000000000 --- a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3Q/V9/MD5E-s1103786--0880b9d68b2cc3bbaced2db301bcc83d.nii.gz/MD5E-s1103786--0880b9d68b2cc3bbaced2db301bcc83d.nii.gz \ No newline at end of file diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 883542246..000000000 --- a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:53:8.382500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997011, - 0.0768685, - 0.00781709, - -0.0690184, - 0.931508, - -0.357112 - ], - "ImageOrientationText": "Tra>Cor(-20.8)>Sag(2.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0459403, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 622, - -7194, - -8810, - 631, - 81, - 16, - -45, - -5 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 249.116, - "WipMemBlock": "df6c19f7-c189-4b5e-966a-d8ab057d416e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 0238a2f64..000000000 --- a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/7X/wZ/MD5E-s1103804--27d29480967ff73b3825312a2437c10f.nii.gz/MD5E-s1103804--27d29480967ff73b3825312a2437c10f.nii.gz \ No newline at end of file diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index b9b6b1e04..000000000 --- a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:02:12.715000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997011, - 0.0768685, - 0.00781709, - -0.0690184, - 0.931508, - -0.357112 - ], - "ImageOrientationText": "Tra>Cor(-20.8)>Sag(2.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0459403, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 622, - -7194, - -8810, - 631, - 81, - 16, - -45, - -5 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 249.116, - "WipMemBlock": "c35b16e6-6e9e-4aa0-806e-1b4c3abe0ff2||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 556df352f..000000000 --- a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Q3/5k/MD5E-s1103846--240325d639e7fa727ab20dd00383ce4e.nii.gz/MD5E-s1103846--240325d639e7fa727ab20dd00383ce4e.nii.gz \ No newline at end of file diff --git a/sub-01/ses-002/sub-01_ses-002_scans.tsv b/sub-01/ses-002/sub-01_ses-002_scans.tsv index 2a60a6b48..e513305c9 120000 --- a/sub-01/ses-002/sub-01_ses-002_scans.tsv +++ b/sub-01/ses-002/sub-01_ses-002_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/Mw/Kf/MD5E-s2667--8762ea3056e44332395a4e15b2fc1611.tsv/MD5E-s2667--8762ea3056e44332395a4e15b2fc1611.tsv \ No newline at end of file +../../.git/annex/objects/GM/MF/MD5E-s2066--a06a121392109e09b9f6d76b562876c7.tsv/MD5E-s2066--a06a121392109e09b9f6d76b562876c7.tsv \ No newline at end of file From fdc9cbfdf6067f27e70b345171e60a35ac837fcd Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:00:43 -0400 Subject: [PATCH 055/463] fix complex event files --- ...g_events.tsv => sub-01_ses-002_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-002_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-002_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-01_ses-002_task-mario3_run-03_events.tsv} | 0 .../func/sub-01_ses-002_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-01_ses-002_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-01/ses-002/func/{sub-01_ses-002_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-002_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-002/func/{sub-01_ses-002_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-002_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-02_part-phase_events.tsv rename sub-01/ses-002/func/{sub-01_ses-002_task-mario3_run-02_part-mag_events.tsv => sub-01_ses-002_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_events.tsv similarity index 100% rename from sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-02_part-mag_events.tsv rename to sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_events.tsv diff --git a/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-mag_events.tsv b/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-002/func/sub-01_ses-002_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 009d040a634b1c7ea74417a8b1f0afbb4ef96c9d Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:02:08 -0400 Subject: [PATCH 056/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-003_acq-axial_localizer.json | 81 +++ .../sub-01_ses-003_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-003_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-003_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-003_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-003_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-003/anat/sub-01_ses-003_scout.json | 542 ++++++++++++++++++ .../ses-003/anat/sub-01_ses-003_scout.nii.gz | 1 + ...3_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-003_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-01_part-mag_events.tsv | 1 + ...003_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-01_part-phase_events.tsv | 1 + ...3_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-003_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-02_part-mag_events.tsv | 1 + ...003_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-02_part-phase_events.tsv | 1 + ...3_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-003_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-03_part-mag_events.tsv | 1 + ...003_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-03_part-phase_events.tsv | 1 + ...3_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-01/ses-003/sub-01_ses-003_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-003/anat/sub-01_ses-003_acq-axial_localizer.json create mode 120000 sub-01/ses-003/anat/sub-01_ses-003_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-003/anat/sub-01_ses-003_acq-coronal_localizer.json create mode 120000 sub-01/ses-003/anat/sub-01_ses-003_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-003/anat/sub-01_ses-003_acq-sagittal_localizer.json create mode 120000 sub-01/ses-003/anat/sub-01_ses-003_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-003/anat/sub-01_ses-003_scout.json create mode 120000 sub-01/ses-003/anat/sub-01_ses-003_scout.nii.gz create mode 100644 sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-01/ses-003/sub-01_ses-003_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 57c079c68..3a8e8be8d 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 57c079c689ac463d492dd48539ba817f5ebc22de +Subproject commit 3a8e8be8d197a3420e8ff46757678018510d5bae diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-003/anat/sub-01_ses-003_acq-axial_localizer.json b/sub-01/ses-003/anat/sub-01_ses-003_acq-axial_localizer.json new file mode 100644 index 000000000..b81f60b45 --- /dev/null +++ b/sub-01/ses-003/anat/sub-01_ses-003_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + 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a/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-phase_events.tsv new file mode 120000 index 000000000..1bbdfddb5 --- /dev/null +++ b/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-phase_events.tsv @@ -0,0 +1 @@ +../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-phase_sbref.json b/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-phase_sbref.json new file mode 100644 index 000000000..62dc1b03f --- /dev/null +++ b/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-phase_sbref.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:48:16.067500", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTime1": 0.037, + "EchoTime2": 0.001, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Single-band reference", + "ImageOrientationPatientDICOM": [ + 0.995275, + 0.094525, + 0.0221887, + -0.0816517, + 0.938488, + -0.335518 + ], + "ImageOrientationText": "Tra>Cor(-19.4)>Sag(3.0)", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "P", + "ND", + "MOSAIC", + "PHASE" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "func_task-mario3_run-03", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0812972, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "SeriesDescription": "func_task-mario3_run-03_SBRef", + "SeriesNumber": 15, + "ShimSetting": [ + 628, + -7198, + -8792, + 645, + 90, + 7, + -22, + 9 + ], + "SliceThickness": 2, + "SliceTiming": [ + 0, + 0.0975, + 0.195, + 0.2925, + 0.39, + 0.4875, + 0.5875, + 0.685, + 0.7825, + 0.88, + 0.9775, + 1.0775, + 1.175, + 1.2725, + 1.37, + 1.4675, + 1.5675, + 1.665, + 1.7625, + 1.86, + 1.9575, + 2.0575, + 2.155, + 2.2525, + 2.35, + 2.4475, + 2.5475, + 2.645, + 2.7425, + 2.84, + 2.9375, + 3.0375, + 3.135, + 3.2325, + 3.33, + 3.4275, + 3.5275, + 3.625, + 3.7225, + 3.82, + 3.9175, + 4.0175, + 4.115, + 4.2125, + 4.31, + 4.4075, + 4.5075, + 4.605, + 4.7025, + 4.8, + 4.8975, + 4.9975, + 5.095, + 5.1925, + 5.29, + 5.3875, + 5.485, + 5.585, + 5.6825, + 5.78 + ], + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 316.058, + "WipMemBlock": "f357e32a-7d2c-4008-8d97-ea108d46e6e2||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-phase_sbref.nii.gz b/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-phase_sbref.nii.gz new file mode 120000 index 000000000..38f5d453d --- /dev/null +++ b/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/J3/2K/MD5E-s1103736--575b57ec4ffb1093ec192db6c748e8bc.nii.gz/MD5E-s1103736--575b57ec4ffb1093ec192db6c748e8bc.nii.gz \ No newline at end of file diff --git a/sub-01/ses-003/sub-01_ses-003_scans.tsv b/sub-01/ses-003/sub-01_ses-003_scans.tsv new file mode 120000 index 000000000..1865f6e46 --- /dev/null +++ b/sub-01/ses-003/sub-01_ses-003_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/jG/x7/MD5E-s2667--985891651e0a24d0cd6e19badc124e26.tsv/MD5E-s2667--985891651e0a24d0cd6e19badc124e26.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..c89c88197 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.995275, 0.094525, 0.0221887, -0.0816517, 0.938488, -0.335518], + "ImageOrientationText": "Tra>Cor(-19.4)>Sag(3.0)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0812972, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [628, -7198, -8792, 645, 90, 7, -22, 9], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 316.058, + "dcmmeta_affine": [ + [-1.9905503988265991, -0.16330337524414062, 0.10507746785879135, 110.75867462158203], + [-0.18905001878738403, 1.876976728439331, -0.6642428040504456, -50.97745132446289], + [0.04437743127346039, 0.6710368394851685, 1.883544683456421, -53.84955596923828], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From c765da4d2b37c2b09bd48621b4be0ae3eb9133a6 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:02:21 -0400 Subject: [PATCH 057/463] fill IntendedFor --- ...1_ses-002_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...1_ses-002_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-002_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...1_ses-002_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_epi.json index 329b4dff2..876592687 100644 --- a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997011, - 0.0768685, - 0.00781709, - -0.0690184, - 0.931508, - -0.357112 - ], + "ImageOrientationPatientDICOM": [0.997011, 0.0768685, 0.00781709, -0.0690184, 0.931508, -0.357112], "ImageOrientationText": "Tra>Cor(-20.8)>Sag(2.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-01_ses-002_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-002/func/sub-01_ses-002_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-002/func/sub-01_ses-002_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 622, - -7194, - -8810, - 631, - 81, - 16, - -45, - -5 - ], + "ShimSetting": [622, -7194, -8810, 631, 81, 16, -45, -5], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_epi.json index f8cd8c111..2f87685e5 100644 --- a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997011, - 0.0768685, - 0.00781709, - -0.0690184, - 0.931508, - -0.357112 - ], + "ImageOrientationPatientDICOM": [0.997011, 0.0768685, 0.00781709, -0.0690184, 0.931508, -0.357112], "ImageOrientationText": "Tra>Cor(-20.8)>Sag(2.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-01_ses-002_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 622, - -7194, - -8810, - 631, - 81, - 16, - -45, - -5 - ], + "ShimSetting": [622, -7194, -8810, 631, 81, 16, -45, -5], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_epi.json index 32f86eb86..fdb661aec 100644 --- a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997011, - 0.0768685, - 0.00781709, - -0.0690184, - 0.931508, - -0.357112 - ], + "ImageOrientationPatientDICOM": [0.997011, 0.0768685, 0.00781709, -0.0690184, 0.931508, -0.357112], "ImageOrientationText": "Tra>Cor(-20.8)>Sag(2.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-01_ses-002_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 622, - -7194, - -8810, - 631, - 81, - 16, - -45, - -5 - ], + "ShimSetting": [622, -7194, -8810, 631, 81, 16, -45, -5], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.02, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_epi.json b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_epi.json index 86a92b47a..ea27b3f6f 100644 --- a/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-01/ses-002/fmap/sub-01_ses-002_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997011, - 0.0768685, - 0.00781709, - -0.0690184, - 0.931508, - -0.357112 - ], + "ImageOrientationPatientDICOM": [0.997011, 0.0768685, 0.00781709, -0.0690184, 0.931508, -0.357112], "ImageOrientationText": "Tra>Cor(-20.8)>Sag(2.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-01_ses-002_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 622, - -7194, - -8810, - 631, - 81, - 16, - -45, - -5 - ], + "ShimSetting": [622, -7194, -8810, 631, 81, 16, -45, -5], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 53b6279bdcc58394e844f450810fc5493a333812 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:03:24 -0400 Subject: [PATCH 058/463] fix fmap phase --- ...1_ses-003_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-003_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-003_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-01/ses-003/sub-01_ses-003_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-01/ses-003/fmap/{sub-01_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-003_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-003/fmap/{sub-01_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-003_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-003/fmap/{sub-01_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-003_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-003/fmap/{sub-01_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-003_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-003/fmap/{sub-01_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-003_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-003/fmap/{sub-01_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-003_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-003/fmap/{sub-01_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-003_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-003/fmap/{sub-01_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-003_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-01/ses-003/fmap/{sub-01_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-01_ses-003_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-01/ses-003/fmap/{sub-01_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-01_ses-003_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 3f76ea2db..000000000 --- a/sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:23:32.600000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.995275, 0.094525, 0.0221887, -0.0816517, 0.938488, -0.335518], - "ImageOrientationText": "Tra>Cor(-19.4)>Sag(3.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0648348, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [628, -7198, -8792, 645, 90, 7, -22, 9], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 316.058, - "WipMemBlock": "01f0a515-cfa9-4301-ad1f-c69652cbd5ed||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9905503988265991, -0.16330337524414062, 0.10507746785879135, 110.75867462158203], - [-0.18905001878738403, 1.876976728439331, -0.6642428040504456, -50.97745132446289], - [0.04437743127346039, 0.6710368394851685, 1.883544683456421, -53.84955596923828], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99527517946697, 0.09452501254459, 0.02218871651163, -0.0816516906238, 0.93848835867708, -0.3355184079091], - "ImagePositionPatient": [-759.05632648923, -894.38488379808, 243.37124959283], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.25879, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "112134.106000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.06483479935981, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "112418.780000", - "SliceLocation": -27.964198450415, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000696305, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "112134.007000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["112332.600000", "112334.090000", "112335.580000"], - "ContentTime": ["112418.782000", "112418.785000", "112418.788000"], - "InstanceCreationTime": ["112418.782000", "112418.785000", "112418.788000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4870.0, 4872.0, 4870.0], - "WindowWidth": [18678.0, 18680.0, 18676.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 3f493bd2c..000000000 --- a/sub-01/ses-003/fmap/sub-01_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Qz/pV/MD5E-s3334999--db8654325641da8fa7339754d8753b0a.nii.gz/MD5E-s3334999--db8654325641da8fa7339754d8753b0a.nii.gz \ No newline at end of file diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index d242dc13d..000000000 --- a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:23:22.170000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995275, - 0.094525, - 0.0221887, - -0.0816517, - 0.938488, - -0.335518 - ], - "ImageOrientationText": "Tra>Cor(-19.4)>Sag(3.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0648348, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 628, - -7198, - -8792, - 645, - 90, - 7, - -22, - 9 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 316.058, - "WipMemBlock": "01f0a515-cfa9-4301-ad1f-c69652cbd5ed||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 6d46bb441..000000000 --- a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/6V/58/MD5E-s1112363--43a369825fca57aac7980c1e94a040fe.nii.gz/MD5E-s1112363--43a369825fca57aac7980c1e94a040fe.nii.gz \ No newline at end of file diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 486952cde..000000000 --- a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:26:5.652500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995275, - 0.094525, - 0.0221887, - -0.0816517, - 0.938488, - -0.335518 - ], - "ImageOrientationText": "Tra>Cor(-19.4)>Sag(3.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0812972, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 628, - -7198, - -8792, - 645, - 90, - 7, - -22, - 9 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 316.058, - "WipMemBlock": "39360ec6-722a-4622-b620-e302a6ea47b7||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 309439b9b..000000000 --- a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/91/G0/MD5E-s1103944--1673a6d0b0af028f97aa7eeb5841b88b.nii.gz/MD5E-s1103944--1673a6d0b0af028f97aa7eeb5841b88b.nii.gz \ No newline at end of file diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 8f121e486..000000000 --- a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:37:11.370000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995275, - 0.094525, - 0.0221887, - -0.0816517, - 0.938488, - -0.335518 - ], - "ImageOrientationText": "Tra>Cor(-19.4)>Sag(3.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0812972, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 628, - -7198, - -8792, - 645, - 90, - 7, - -22, - 9 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 316.058, - "WipMemBlock": "65ac1950-c6c6-4e01-9476-f9dd1ade0a38||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 19afda85a..000000000 --- a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/w4/Vz/MD5E-s1103908--2a5c0d438a1c70358c76629726e4e612.nii.gz/MD5E-s1103908--2a5c0d438a1c70358c76629726e4e612.nii.gz \ No newline at end of file diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 50e4ac347..000000000 --- a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:48:16.067500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995275, - 0.094525, - 0.0221887, - -0.0816517, - 0.938488, - -0.335518 - ], - "ImageOrientationText": "Tra>Cor(-19.4)>Sag(3.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0812972, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 628, - -7198, - -8792, - 645, - 90, - 7, - -22, - 9 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 316.058, - "WipMemBlock": "f357e32a-7d2c-4008-8d97-ea108d46e6e2||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 38f5d453d..000000000 --- a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/J3/2K/MD5E-s1103736--575b57ec4ffb1093ec192db6c748e8bc.nii.gz/MD5E-s1103736--575b57ec4ffb1093ec192db6c748e8bc.nii.gz \ No newline at end of file diff --git a/sub-01/ses-003/sub-01_ses-003_scans.tsv b/sub-01/ses-003/sub-01_ses-003_scans.tsv index 1865f6e46..015826660 120000 --- a/sub-01/ses-003/sub-01_ses-003_scans.tsv +++ b/sub-01/ses-003/sub-01_ses-003_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/jG/x7/MD5E-s2667--985891651e0a24d0cd6e19badc124e26.tsv/MD5E-s2667--985891651e0a24d0cd6e19badc124e26.tsv \ No newline at end of file +../../.git/annex/objects/V6/VM/MD5E-s2066--b8a08d5347178c407d8b6bc70ab90baa.tsv/MD5E-s2066--b8a08d5347178c407d8b6bc70ab90baa.tsv \ No newline at end of file From ace3e5760a3ba8a39d21e8ee106af7736cb49756 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:03:33 -0400 Subject: [PATCH 059/463] fix complex event files --- ...g_events.tsv => sub-01_ses-003_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-003_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-003_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-01_ses-003_task-mario3_run-03_events.tsv} | 0 .../func/sub-01_ses-003_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-01_ses-003_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-01/ses-003/func/{sub-01_ses-003_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-003_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-003/func/{sub-01_ses-003_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-003_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-02_part-phase_events.tsv rename sub-01/ses-003/func/{sub-01_ses-003_task-mario3_run-02_part-mag_events.tsv => sub-01_ses-003_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_events.tsv similarity index 100% rename from sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-02_part-mag_events.tsv rename to sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_events.tsv diff --git a/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-mag_events.tsv b/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-003/func/sub-01_ses-003_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From ba4505973333c42edba3fa2a078b462db712757a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:04:53 -0400 Subject: [PATCH 060/463] fill IntendedFor --- ...1_ses-003_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...1_ses-003_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-003_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...1_ses-003_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_epi.json index 295afee04..f810cef3e 100644 --- a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995275, - 0.094525, - 0.0221887, - -0.0816517, - 0.938488, - -0.335518 - ], + "ImageOrientationPatientDICOM": [0.995275, 0.094525, 0.0221887, -0.0816517, 0.938488, -0.335518], "ImageOrientationText": "Tra>Cor(-19.4)>Sag(3.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-01_ses-003_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-003/func/sub-01_ses-003_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-003/func/sub-01_ses-003_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 628, - -7198, - -8792, - 645, - 90, - 7, - -22, - 9 - ], + "ShimSetting": [628, -7198, -8792, 645, 90, 7, -22, 9], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_epi.json index 91f389f59..0e7140bd9 100644 --- a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995275, - 0.094525, - 0.0221887, - -0.0816517, - 0.938488, - -0.335518 - ], + "ImageOrientationPatientDICOM": [0.995275, 0.094525, 0.0221887, -0.0816517, 0.938488, -0.335518], "ImageOrientationText": "Tra>Cor(-19.4)>Sag(3.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-01_ses-003_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 628, - -7198, - -8792, - 645, - 90, - 7, - -22, - 9 - ], + "ShimSetting": [628, -7198, -8792, 645, 90, 7, -22, 9], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_epi.json index fb8518ada..cb661d0aa 100644 --- a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995275, - 0.094525, - 0.0221887, - -0.0816517, - 0.938488, - -0.335518 - ], + "ImageOrientationPatientDICOM": [0.995275, 0.094525, 0.0221887, -0.0816517, 0.938488, -0.335518], "ImageOrientationText": "Tra>Cor(-19.4)>Sag(3.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-01_ses-003_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 628, - -7198, - -8792, - 645, - 90, - 7, - -22, - 9 - ], + "ShimSetting": [628, -7198, -8792, 645, 90, 7, -22, 9], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_epi.json b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_epi.json index d1798699d..9c7f47683 100644 --- a/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-01/ses-003/fmap/sub-01_ses-003_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995275, - 0.094525, - 0.0221887, - -0.0816517, - 0.938488, - -0.335518 - ], + "ImageOrientationPatientDICOM": [0.995275, 0.094525, 0.0221887, -0.0816517, 0.938488, -0.335518], "ImageOrientationText": "Tra>Cor(-19.4)>Sag(3.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-01_ses-003_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 628, - -7198, - -8792, - 645, - 90, - 7, - -22, - 9 - ], + "ShimSetting": [628, -7198, -8792, 645, 90, 7, -22, 9], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.4875, 0.5875, 0.685, 0.7825, 0.88, 0.9775, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.485, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 82bf55134ce9d279af844fcae82a0f6acbc70d5c Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:06:25 -0400 Subject: [PATCH 061/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..10186d9a0 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = c1fa5a96-0cc7-4b7d-a00b-9a4b5dd71b80 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..48279dba9 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 48279dba905c498b0895be513dc43398e5792da4 From e183807ac8b6ce0275bf8dc93db9889f13d16614 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:06:55 -0400 Subject: [PATCH 062/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-007_acq-axial_localizer.json | 81 +++ .../sub-02_ses-007_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-007_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-007_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-007_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-007_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-007/anat/sub-02_ses-007_scout.json | 542 ++++++++++++++++++ .../ses-007/anat/sub-02_ses-007_scout.nii.gz | 1 + ...7_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-007_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...07_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...007_task-mario3_run-01_part-mag_events.tsv | 1 + ...007_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...07_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-01_part-phase_events.tsv | 1 + ...7_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-007_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...07_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...007_task-mario3_run-02_part-mag_events.tsv | 1 + ...007_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...07_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-02_part-phase_events.tsv | 1 + ...7_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-007_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...07_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...007_task-mario3_run-03_part-mag_events.tsv | 1 + ...007_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...07_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-03_part-phase_events.tsv | 1 + ...7_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-02/ses-007/sub-02_ses-007_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-007/anat/sub-02_ses-007_acq-axial_localizer.json create mode 120000 sub-02/ses-007/anat/sub-02_ses-007_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-007/anat/sub-02_ses-007_acq-coronal_localizer.json create mode 120000 sub-02/ses-007/anat/sub-02_ses-007_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-007/anat/sub-02_ses-007_acq-sagittal_localizer.json create mode 120000 sub-02/ses-007/anat/sub-02_ses-007_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-007/anat/sub-02_ses-007_scout.json create mode 120000 sub-02/ses-007/anat/sub-02_ses-007_scout.nii.gz create mode 100644 sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 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sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-02/ses-007/sub-02_ses-007_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index a165b19b2..67865494f 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit a165b19b23509af4683e378494dbed466f2e50c1 +Subproject commit 67865494fabc677536c4a9657f32c983346ed1e2 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..83ada7a9d --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 51 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-007/anat/sub-02_ses-007_acq-axial_localizer.json b/sub-02/ses-007/anat/sub-02_ses-007_acq-axial_localizer.json new file mode 100644 index 000000000..bfeb0d7d1 --- /dev/null +++ b/sub-02/ses-007/anat/sub-02_ses-007_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:18:7.052500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + 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000000000..01e2f5144 --- /dev/null +++ b/sub-02/ses-007/anat/sub-02_ses-007_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:18:14.042500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + 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"TxRefAmp": 284.32, + "dcmmeta_affine": [ + [-1.9982565641403198, 0.03732188418507576, 0.07468599826097488, 103.40579986572266], + [-0.009304900653660297, 1.6783627271652222, -1.0876635313034058, -46.9048957824707], + [0.08297192305326462, 1.0870628356933594, 1.67672598361969, -89.04330444335938], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From d2df2bcfd231aaabcc8f6d2a605f654db98ab4ab Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:07:23 -0400 Subject: [PATCH 063/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-001_acq-axial_localizer.json | 81 +++ .../sub-02_ses-001_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-001_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-001_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-001_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-001_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-001/anat/sub-02_ses-001_scout.json | 542 ++++++++++++++++++ .../ses-001/anat/sub-02_ses-001_scout.nii.gz | 1 + ...1_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-001_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-01_part-mag_events.tsv | 1 + ...001_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-01_part-phase_events.tsv | 1 + ...1_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-001_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-02_part-mag_events.tsv | 1 + ...001_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-02_part-phase_events.tsv | 1 + ...1_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-001_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-03_part-mag_events.tsv | 1 + ...001_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-03_part-phase_events.tsv | 1 + ...1_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-001_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-04_part-mag_events.tsv | 1 + ...001_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-04_part-phase_events.tsv | 1 + ...1_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-02/ses-001/sub-02_ses-001_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5409 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-001/anat/sub-02_ses-001_acq-axial_localizer.json create mode 120000 sub-02/ses-001/anat/sub-02_ses-001_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-001/anat/sub-02_ses-001_acq-coronal_localizer.json create mode 120000 sub-02/ses-001/anat/sub-02_ses-001_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-001/anat/sub-02_ses-001_acq-sagittal_localizer.json create mode 120000 sub-02/ses-001/anat/sub-02_ses-001_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-001/anat/sub-02_ses-001_scout.json create mode 120000 sub-02/ses-001/anat/sub-02_ses-001_scout.nii.gz create mode 100644 sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_part-phase_sbref.nii.gz create mode 120000 sub-02/ses-001/sub-02_ses-001_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 8f66f116c..424ac18bc 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 8f66f116cda552f24480c3ca773ae82d059e86c8 +Subproject commit 424ac18bc707aae9ddb7f777a35957fc7b7fa168 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..83ada7a9d --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 51 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-001/anat/sub-02_ses-001_acq-axial_localizer.json b/sub-02/ses-001/anat/sub-02_ses-001_acq-axial_localizer.json new file mode 100644 index 000000000..e93abc276 --- /dev/null +++ b/sub-02/ses-001/anat/sub-02_ses-001_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:17:22.040000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0339156, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 269.272 +} \ No newline at end of file diff --git a/sub-02/ses-001/anat/sub-02_ses-001_acq-axial_localizer.nii.gz b/sub-02/ses-001/anat/sub-02_ses-001_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..a9010e987 --- /dev/null +++ b/sub-02/ses-001/anat/sub-02_ses-001_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/gq/59/MD5E-s181849--495f7ca670822044204c35209b26d43d.nii.gz/MD5E-s181849--495f7ca670822044204c35209b26d43d.nii.gz \ No newline at end of file diff --git a/sub-02/ses-001/anat/sub-02_ses-001_acq-coronal_localizer.json b/sub-02/ses-001/anat/sub-02_ses-001_acq-coronal_localizer.json new file mode 100644 index 000000000..ea14587ff --- /dev/null +++ b/sub-02/ses-001/anat/sub-02_ses-001_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:17:29.030000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0339156, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 269.272 +} \ No newline at end of file diff --git a/sub-02/ses-001/anat/sub-02_ses-001_acq-coronal_localizer.nii.gz b/sub-02/ses-001/anat/sub-02_ses-001_acq-coronal_localizer.nii.gz new file mode 120000 index 000000000..4887336f3 --- /dev/null +++ b/sub-02/ses-001/anat/sub-02_ses-001_acq-coronal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/v1/F4/MD5E-s192283--ed5b360ab00519dd5cb2d4fceb439be7.nii.gz/MD5E-s192283--ed5b360ab00519dd5cb2d4fceb439be7.nii.gz \ No newline at end of file diff --git a/sub-02/ses-001/anat/sub-02_ses-001_acq-sagittal_localizer.json b/sub-02/ses-001/anat/sub-02_ses-001_acq-sagittal_localizer.json new file mode 100644 index 000000000..b5452b85d --- /dev/null +++ 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101.86430358886719], + [0.0013938124757260084, 1.708186388015747, -1.0402390956878662, -49.90155029296875], + [0.1256946474313736, 1.0381081104278564, 1.7048555612564087, -106.11486053466797], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 0517ba4c1fb81e2fc29bdb4feb20f658c0a7c3a3 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:07:40 -0400 Subject: [PATCH 064/463] fix fmap phase --- ...2_ses-007_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-007_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-007_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-007_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-007_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-007_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-02/ses-007/sub-02_ses-007_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-02/ses-007/fmap/{sub-02_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-007_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-007/fmap/{sub-02_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-007_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-007/fmap/{sub-02_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-007_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-007/fmap/{sub-02_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-007_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-007/fmap/{sub-02_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-007_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-007/fmap/{sub-02_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-007_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-007/fmap/{sub-02_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-007_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-007/fmap/{sub-02_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-007_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-007/fmap/{sub-02_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-007_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-007/fmap/{sub-02_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-007_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index f0d6cf5d9..000000000 --- a/sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:19:9.680000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999128, 0.00465245, 0.041486, 0.0186609, 0.839181, -0.543531], - "ImageOrientationText": "Tra>Cor(-33.0)>Sag(2.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - 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"BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.9991282548604, 0.00465245024183, 0.04148596203963, 0.01866094206303, 0.83918136335533, -0.5435314237819], - "ImagePositionPatient": [-848.20049272637, -740.27748132592, 388.41326139493], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.258973, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "161716.389000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.04940671101223, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "161955.564000", - "SliceLocation": -45.280758816488, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999512387, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "161716.323000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["161909.680000", "161911.170000", "161912.660000"], - "ContentTime": ["161955.566000", "161955.568000", "161955.571000"], - "InstanceCreationTime": ["161955.566000", "161955.568000", "161955.571000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4722.0, 4722.0, 4744.0], - "WindowWidth": [18556.0, 18546.0, 18584.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index bf1268096..000000000 --- a/sub-02/ses-007/fmap/sub-02_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/50/0Q/MD5E-s3333737--4ba510b996e6bf05d7ccdf961f2ec612.nii.gz/MD5E-s3333737--4ba510b996e6bf05d7ccdf961f2ec612.nii.gz \ No newline at end of file diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index e13733f03..000000000 --- a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:18:59.250000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999128, - 0.00465245, - 0.041486, - 0.0186609, - 0.839181, - -0.543531 - ], - "ImageOrientationText": "Tra>Cor(-33.0)>Sag(2.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0494067, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 622, - -7187, - -8873, - 225, - 23, - -215, - -2, - 21 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 284.32, - "WipMemBlock": "21900d6c-77ab-4bf8-8736-2c48a1e6c096||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index c5a07e95f..000000000 --- a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3q/g1/MD5E-s1112080--8bc358f2db63af1191bfd6b065daafb0.nii.gz/MD5E-s1112080--8bc358f2db63af1191bfd6b065daafb0.nii.gz \ No newline at end of file diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index af670eb9e..000000000 --- a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:20:14.550000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999128, - 0.00465245, - 0.041486, - 0.0186609, - 0.839181, - -0.543531 - ], - "ImageOrientationText": "Tra>Cor(-33.0)>Sag(2.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0619517, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 622, - -7187, - -8873, - 225, - 23, - -215, - -2, - 21 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 284.32, - "WipMemBlock": "2410f030-a484-4357-ae7c-6f04bb95500a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index cb28596c2..000000000 --- a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/fw/gX/MD5E-s1103155--4634488aee1b4731eda4d7b73662f347.nii.gz/MD5E-s1103155--4634488aee1b4731eda4d7b73662f347.nii.gz \ No newline at end of file diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 88b9ef653..000000000 --- a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:30:45.542500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999128, - 0.00465245, - 0.041486, - 0.0186609, - 0.839181, - -0.543531 - ], - "ImageOrientationText": "Tra>Cor(-33.0)>Sag(2.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0619517, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 622, - -7187, - -8873, - 225, - 23, - -215, - -2, - 21 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 284.32, - "WipMemBlock": "ac30b1af-3025-44a7-b1df-9373305f52b0||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index f55c52df8..000000000 --- a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Zw/xm/MD5E-s1103191--7d68cd781805d06474bd5b3c8b978321.nii.gz/MD5E-s1103191--7d68cd781805d06474bd5b3c8b978321.nii.gz \ No newline at end of file diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index a81d44205..000000000 --- a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:39:28.575000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999128, - 0.00465245, - 0.041486, - 0.0186609, - 0.839181, - -0.543531 - ], - "ImageOrientationText": "Tra>Cor(-33.0)>Sag(2.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0619517, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 622, - -7187, - -8873, - 225, - 23, - -215, - -2, - 21 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 284.32, - "WipMemBlock": "1001c8ee-7f43-4e78-8e96-8491b44b7da9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 30c4271cb..000000000 --- a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/kF/M9/MD5E-s1103356--4bd838ba5566ccedc4807c3f6ec84307.nii.gz/MD5E-s1103356--4bd838ba5566ccedc4807c3f6ec84307.nii.gz \ No newline at end of file diff --git a/sub-02/ses-007/sub-02_ses-007_scans.tsv b/sub-02/ses-007/sub-02_ses-007_scans.tsv index df3e845be..63dea2715 120000 --- a/sub-02/ses-007/sub-02_ses-007_scans.tsv +++ b/sub-02/ses-007/sub-02_ses-007_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/px/J9/MD5E-s2667--f69f7fcb4e55acc185796505eb8cf832.tsv/MD5E-s2667--f69f7fcb4e55acc185796505eb8cf832.tsv \ No newline at end of file +../../.git/annex/objects/K9/wp/MD5E-s2066--7118badbaed60f4ae11c01b0393fd821.tsv/MD5E-s2066--7118badbaed60f4ae11c01b0393fd821.tsv \ No newline at end of file From 42e5e644b0e4580057a952e62b99aa6b1dda4e0d Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:07:57 -0400 Subject: [PATCH 065/463] fix complex event files --- ...g_events.tsv => sub-02_ses-007_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-02_ses-007_task-mario3_run-02_events.tsv} | 0 .../func/sub-02_ses-007_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-02_ses-007_task-mario3_run-03_events.tsv} | 0 .../func/sub-02_ses-007_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-02_ses-007_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-02/ses-007/func/{sub-02_ses-007_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-007_task-mario3_run-01_events.tsv} (100%) rename sub-02/ses-007/func/{sub-02_ses-007_task-mario3_run-01_part-phase_events.tsv => sub-02_ses-007_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-02_part-phase_events.tsv rename sub-02/ses-007/func/{sub-02_ses-007_task-mario3_run-02_part-mag_events.tsv => sub-02_ses-007_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-02_events.tsv similarity index 100% rename from sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-01_part-phase_events.tsv rename to sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-02_events.tsv diff --git a/sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-02_part-phase_events.tsv b/sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-02_part-mag_events.tsv b/sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_events.tsv similarity index 100% rename from sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-02_part-mag_events.tsv rename to sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_events.tsv diff --git a/sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_part-mag_events.tsv b/sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-007/func/sub-02_ses-007_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 2a0e2883bd83b0888ced3b2293e6d23b8b28d4da Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:08:24 -0400 Subject: [PATCH 066/463] fix fmap phase --- ...2_ses-001_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-001_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-001_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-02/ses-001/sub-02_ses-001_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-02/ses-001/fmap/{sub-02_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-001_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-001/fmap/{sub-02_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-001_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-001/fmap/{sub-02_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-001_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-001/fmap/{sub-02_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-001_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-001/fmap/{sub-02_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-001_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-001/fmap/{sub-02_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-001_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-001/fmap/{sub-02_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-001_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-001/fmap/{sub-02_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-001_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-001/fmap/{sub-02_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-001_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-001/fmap/{sub-02_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-001_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-02/ses-001/fmap/{sub-02_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-02_ses-001_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-02/ses-001/fmap/{sub-02_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-02_ses-001_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 22c873f2a..000000000 --- a/sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:18:24.410000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.998023, -0.000696906, 0.0628473, 0.0332822, 0.854093, -0.519054], - "ImageOrientationText": "Tra>Cor(-31.4)>Sag(3.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - 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"func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "161909.978000", - "SliceLocation": -59.069509977581, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999824391, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "161631.066000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["161824.410000", "161825.900000", "161827.390000"], - "ContentTime": ["161909.980000", "161909.982000", "161909.985000"], - "InstanceCreationTime": ["161909.980000", "161909.982000", "161909.985000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4780.0, 4782.0, 4780.0], - "WindowWidth": [18580.0, 18582.0, 18578.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index bca19edea..000000000 --- a/sub-02/ses-001/fmap/sub-02_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/k9/Pz/MD5E-s3332253--63f69da9637ccf1a4ef53c44cb4aeede.nii.gz/MD5E-s3332253--63f69da9637ccf1a4ef53c44cb4aeede.nii.gz \ No newline at end of file diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 615be8552..000000000 --- a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:18:13.980000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998023, - -0.000696906, - 0.0628473, - 0.0332822, - 0.854093, - -0.519054 - ], - "ImageOrientationText": "Tra>Cor(-31.4)>Sag(3.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0398387, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 633, - -7188, - -8880, - 298, - 24, - -168, - 3, - 48 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 269.272, - "WipMemBlock": "f30727de-8c5b-41eb-8a4f-83afbeb58531||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index fd991da23..000000000 --- a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/G2/5p/MD5E-s1112004--722ccb94dc07154ff6d0188cc8485c6a.nii.gz/MD5E-s1112004--722ccb94dc07154ff6d0188cc8485c6a.nii.gz \ No newline at end of file diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index b3806fcde..000000000 --- a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:19:46.657500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": 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- "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0499543, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 633, - -7188, - -8880, - 298, - 24, - -168, - 3, - 48 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 269.272, - "WipMemBlock": "1eb20d0a-8120-43f4-ad3c-9ea79f09e619||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index b69fe034b..000000000 --- a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/9k/k5/MD5E-s1103458--26e007d5a8037e33c86178cae9ebfdcb.nii.gz/MD5E-s1103458--26e007d5a8037e33c86178cae9ebfdcb.nii.gz \ No newline at end of file diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 59b7b20c0..000000000 --- a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:29:31.540000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998023, - -0.000696906, - 0.0628473, - 0.0332822, - 0.854093, - -0.519054 - ], - "ImageOrientationText": 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"RepetitionTime": 1.49, - "SAR": 0.0499543, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 633, - -7188, - -8880, - 298, - 24, - -168, - 3, - 48 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 269.272, - "WipMemBlock": "ca506fd9-d3b1-4f7a-a476-8d6e4c37c90e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 5fa728fa8..000000000 --- a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/6F/jz/MD5E-s1103459--94f0cfb6a99d5e1291d208316bb07dd9.nii.gz/MD5E-s1103459--94f0cfb6a99d5e1291d208316bb07dd9.nii.gz \ No newline at end of file diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 1cb2b5a4b..000000000 --- a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:38:45.015000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998023, - -0.000696906, - 0.0628473, - 0.0332822, - 0.854093, - -0.519054 - ], - "ImageOrientationText": "Tra>Cor(-31.4)>Sag(3.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0499543, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 633, - -7188, - -8880, - 298, - 24, - -168, - 3, - 48 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 269.272, - "WipMemBlock": "772971eb-5b2a-418f-9298-40cebf28e75a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 3a6ea670d..000000000 --- a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/PZ/XM/MD5E-s1103219--e48189f2bfe8026fcbe3c60af3ca42ab.nii.gz/MD5E-s1103219--e48189f2bfe8026fcbe3c60af3ca42ab.nii.gz \ No newline at end of file diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 21e654522..000000000 --- a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:47:30.900000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998023, - -0.000696906, - 0.0628473, - 0.0332822, - 0.854093, - -0.519054 - ], - "ImageOrientationText": "Tra>Cor(-31.4)>Sag(3.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0499543, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 633, - -7188, - -8880, - 298, - 24, - -168, - 3, - 48 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 269.272, - "WipMemBlock": "6bfa80c9-8e53-4d7c-a7a1-910f4bdaa40e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index cfc663a4e..000000000 --- a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/X1/2G/MD5E-s1103484--e32f1fdddff7c93bc49b66bc51cf7976.nii.gz/MD5E-s1103484--e32f1fdddff7c93bc49b66bc51cf7976.nii.gz \ No newline at end of file diff --git a/sub-02/ses-001/sub-02_ses-001_scans.tsv b/sub-02/ses-001/sub-02_ses-001_scans.tsv index d2de12579..dc7b41c29 120000 --- a/sub-02/ses-001/sub-02_ses-001_scans.tsv +++ b/sub-02/ses-001/sub-02_ses-001_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/8J/m2/MD5E-s3289--f5a0ce94c104993e0aea0751a8312ffa.tsv/MD5E-s3289--f5a0ce94c104993e0aea0751a8312ffa.tsv \ No newline at end of file +../../.git/annex/objects/x9/jw/MD5E-s2567--27221b82909fb1c391f9bc0406997a2f.tsv/MD5E-s2567--27221b82909fb1c391f9bc0406997a2f.tsv \ No newline at end of file From 57a8933d1f1c638b25d9718880e064a62d2c8fc3 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:08:34 -0400 Subject: [PATCH 067/463] fix complex event files --- ...g_events.tsv => sub-02_ses-001_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-02_ses-001_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-02_ses-001_task-mario3_run-03_events.tsv} | 0 .../func/sub-02_ses-001_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-02_ses-001_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-02_ses-001_task-mario3_run-04_events.tsv} | 0 .../func/sub-02_ses-001_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-02_ses-001_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-02/ses-001/func/{sub-02_ses-001_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-001_task-mario3_run-01_events.tsv} (100%) rename sub-02/ses-001/func/{sub-02_ses-001_task-mario3_run-01_part-phase_events.tsv => sub-02_ses-001_task-mario3_run-02_events.tsv} (100%) rename sub-02/ses-001/func/{sub-02_ses-001_task-mario3_run-02_part-mag_events.tsv => sub-02_ses-001_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_part-phase_events.tsv rename sub-02/ses-001/func/{sub-02_ses-001_task-mario3_run-02_part-phase_events.tsv => sub-02_ses-001_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-02_events.tsv similarity index 100% rename from sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-01_part-phase_events.tsv rename to sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-02_events.tsv diff --git a/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-02_part-mag_events.tsv b/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_events.tsv similarity index 100% rename from sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-02_part-mag_events.tsv rename to sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_events.tsv diff --git a/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_part-mag_events.tsv b/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-02_part-phase_events.tsv b/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_events.tsv similarity index 100% rename from sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-02_part-phase_events.tsv rename to sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_events.tsv diff --git a/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_part-mag_events.tsv b/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_part-phase_events.tsv b/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-001/func/sub-02_ses-001_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From bd5387acabcdf0d04c9ffb0ca4a0fca04f257037 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:10:38 -0400 Subject: [PATCH 068/463] fill IntendedFor --- ...2_ses-007_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...2_ses-007_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...2_ses-007_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...2_ses-007_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_epi.json index 14224551e..e6545956f 100644 --- a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999128, - 0.00465245, - 0.041486, - 0.0186609, - 0.839181, - -0.543531 - ], + "ImageOrientationPatientDICOM": [0.999128, 0.00465245, 0.041486, 0.0186609, 0.839181, -0.543531], "ImageOrientationText": "Tra>Cor(-33.0)>Sag(2.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-02_ses-007_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-007/func/sub-02_ses-007_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-007/func/sub-02_ses-007_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 622, - -7187, - -8873, - 225, - 23, - -215, - -2, - 21 - ], + "ShimSetting": [622, -7187, -8873, 225, 23, -215, -2, 21], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_epi.json b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_epi.json index 29891c6ee..1bf51bba8 100644 --- a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999128, - 0.00465245, - 0.041486, - 0.0186609, - 0.839181, - -0.543531 - ], + "ImageOrientationPatientDICOM": [0.999128, 0.00465245, 0.041486, 0.0186609, 0.839181, -0.543531], "ImageOrientationText": "Tra>Cor(-33.0)>Sag(2.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-02_ses-007_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 622, - -7187, - -8873, - 225, - 23, - -215, - -2, - 21 - ], + "ShimSetting": [622, -7187, -8873, 225, 23, -215, -2, 21], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_epi.json b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_epi.json index 4443fe742..4ff267580 100644 --- a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999128, - 0.00465245, - 0.041486, - 0.0186609, - 0.839181, - -0.543531 - ], + "ImageOrientationPatientDICOM": [0.999128, 0.00465245, 0.041486, 0.0186609, 0.839181, -0.543531], "ImageOrientationText": "Tra>Cor(-33.0)>Sag(2.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-02_ses-007_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 622, - -7187, - -8873, - 225, - 23, - -215, - -2, - 21 - ], + "ShimSetting": [622, -7187, -8873, 225, 23, -215, -2, 21], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_epi.json b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_epi.json index ea5c4e74f..f2d753f0b 100644 --- a/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-02/ses-007/fmap/sub-02_ses-007_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999128, - 0.00465245, - 0.041486, - 0.0186609, - 0.839181, - -0.543531 - ], + "ImageOrientationPatientDICOM": [0.999128, 0.00465245, 0.041486, 0.0186609, 0.839181, -0.543531], "ImageOrientationText": "Tra>Cor(-33.0)>Sag(2.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-02_ses-007_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 622, - -7187, - -8873, - 225, - 23, - -215, - -2, - 21 - ], + "ShimSetting": [622, -7187, -8873, 225, 23, -215, -2, 21], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From f5b7b123d8ce0f5ffcb1fafb1c49ec704f293006 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:11:37 -0400 Subject: [PATCH 069/463] fill IntendedFor --- ...2_ses-001_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...2_ses-001_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...2_ses-001_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...2_ses-001_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...2_ses-001_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_epi.json index 6cabec957..d44d2c728 100644 --- a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998023, - -0.000696906, - 0.0628473, - 0.0332822, - 0.854093, - -0.519054 - ], + "ImageOrientationPatientDICOM": [0.998023, -0.000696906, 0.0628473, 0.0332822, 0.854093, -0.519054], "ImageOrientationText": "Tra>Cor(-31.4)>Sag(3.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-02_ses-001_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-001/func/sub-02_ses-001_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-001/func/sub-02_ses-001_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-001/func/sub-02_ses-001_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 633, - -7188, - -8880, - 298, - 24, - -168, - 3, - 48 - ], + "ShimSetting": [633, -7188, -8880, 298, 24, -168, 3, 48], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_epi.json b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_epi.json index 5bd78336b..dced92a6e 100644 --- a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998023, - -0.000696906, - 0.0628473, - 0.0332822, - 0.854093, - -0.519054 - ], + "ImageOrientationPatientDICOM": [0.998023, -0.000696906, 0.0628473, 0.0332822, 0.854093, -0.519054], "ImageOrientationText": "Tra>Cor(-31.4)>Sag(3.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-02_ses-001_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 633, - -7188, - -8880, - 298, - 24, - -168, - 3, - 48 - ], + "ShimSetting": [633, -7188, -8880, 298, 24, -168, 3, 48], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_epi.json b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_epi.json index 2de3a3e0e..937a7e63d 100644 --- a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998023, - -0.000696906, - 0.0628473, - 0.0332822, - 0.854093, - -0.519054 - ], + "ImageOrientationPatientDICOM": [0.998023, -0.000696906, 0.0628473, 0.0332822, 0.854093, -0.519054], "ImageOrientationText": "Tra>Cor(-31.4)>Sag(3.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-02_ses-001_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 633, - -7188, - -8880, - 298, - 24, - -168, - 3, - 48 - ], + "ShimSetting": [633, -7188, -8880, 298, 24, -168, 3, 48], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_epi.json b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_epi.json index 53aba4891..05a893212 100644 --- a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998023, - -0.000696906, - 0.0628473, - 0.0332822, - 0.854093, - -0.519054 - ], + "ImageOrientationPatientDICOM": [0.998023, -0.000696906, 0.0628473, 0.0332822, 0.854093, -0.519054], "ImageOrientationText": "Tra>Cor(-31.4)>Sag(3.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-02_ses-001_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 633, - -7188, - -8880, - 298, - 24, - -168, - 3, - 48 - ], + "ShimSetting": [633, -7188, -8880, 298, 24, -168, 3, 48], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_epi.json b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_epi.json index ccc2573dd..14a563f1d 100644 --- a/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-02/ses-001/fmap/sub-02_ses-001_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998023, - -0.000696906, - 0.0628473, - 0.0332822, - 0.854093, - -0.519054 - ], + "ImageOrientationPatientDICOM": [0.998023, -0.000696906, 0.0628473, 0.0332822, 0.854093, -0.519054], "ImageOrientationText": "Tra>Cor(-31.4)>Sag(3.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-02_ses-001_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 633, - -7188, - -8880, - 298, - 24, - -168, - 3, - 48 - ], + "ShimSetting": [633, -7188, -8880, 298, 24, -168, 3, 48], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From af1e7e36bb49c24c9c2f50c394efe72d07efce06 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:13:15 -0400 Subject: [PATCH 070/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-003_acq-axial_localizer.json | 81 +++ .../sub-02_ses-003_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-003_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-003_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-003_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-003_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-003/anat/sub-02_ses-003_scout.json | 542 ++++++++++++++++++ .../ses-003/anat/sub-02_ses-003_scout.nii.gz | 1 + ...3_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-003_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-01_part-mag_events.tsv | 1 + ...003_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-01_part-phase_events.tsv | 1 + ...3_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-003_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-02_part-mag_events.tsv | 1 + ...003_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-02_part-phase_events.tsv | 1 + ...3_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-003_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-03_part-mag_events.tsv | 1 + ...003_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-03_part-phase_events.tsv | 1 + ...3_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-02/ses-003/sub-02_ses-003_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-003/anat/sub-02_ses-003_acq-axial_localizer.json create mode 120000 sub-02/ses-003/anat/sub-02_ses-003_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-003/anat/sub-02_ses-003_acq-coronal_localizer.json create mode 120000 sub-02/ses-003/anat/sub-02_ses-003_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-003/anat/sub-02_ses-003_acq-sagittal_localizer.json create mode 120000 sub-02/ses-003/anat/sub-02_ses-003_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-003/anat/sub-02_ses-003_scout.json create mode 120000 sub-02/ses-003/anat/sub-02_ses-003_scout.nii.gz create mode 100644 sub-02/ses-003/fmap/sub-02_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-003/fmap/sub-02_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-003/fmap/sub-02_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-003/fmap/sub-02_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-02/ses-003/sub-02_ses-003_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 21a92023e..d7c0d332e 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 21a92023ed800343fac1176a93a829c8a8e8933d +Subproject commit d7c0d332ed8c9d4b8fb8df7c67fc05deb15d8c00 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..83ada7a9d --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 51 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-003/anat/sub-02_ses-003_acq-axial_localizer.json b/sub-02/ses-003/anat/sub-02_ses-003_acq-axial_localizer.json new file mode 100644 index 000000000..6151e0546 --- /dev/null +++ b/sub-02/ses-003/anat/sub-02_ses-003_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:19:0.075000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": 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103.18023681640625], + [0.013539445586502552, 1.6882197856903076, -1.0722548961639404, -49.090484619140625], + [0.07890652865171432, 1.0709936618804932, 1.6872303485870361, -97.43827056884766], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 43a04060f2d84867ee9d347628e063a08a632e12 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:13:38 -0400 Subject: [PATCH 071/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-022_acq-axial_localizer.json | 81 +++ .../sub-01_ses-022_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-022_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-022_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-022_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-022_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-022/anat/sub-01_ses-022_scout.json | 542 ++++++++++++++++++ .../ses-022/anat/sub-01_ses-022_scout.nii.gz | 1 + ...2_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-022_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...22_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...022_task-mario3_run-01_part-mag_events.tsv | 1 + ...022_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...22_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-01_part-phase_events.tsv | 1 + ...2_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-022_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...22_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...022_task-mario3_run-02_part-mag_events.tsv | 1 + ...022_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...22_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-02_part-phase_events.tsv | 1 + ...2_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-022_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...22_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...022_task-mario3_run-03_part-mag_events.tsv | 1 + ...022_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...22_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-03_part-phase_events.tsv | 1 + ...2_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-01/ses-022/sub-01_ses-022_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-022/anat/sub-01_ses-022_acq-axial_localizer.json create mode 120000 sub-01/ses-022/anat/sub-01_ses-022_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-022/anat/sub-01_ses-022_acq-coronal_localizer.json create mode 120000 sub-01/ses-022/anat/sub-01_ses-022_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-022/anat/sub-01_ses-022_acq-sagittal_localizer.json create mode 120000 sub-01/ses-022/anat/sub-01_ses-022_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-022/anat/sub-01_ses-022_scout.json create mode 120000 sub-01/ses-022/anat/sub-01_ses-022_scout.nii.gz create mode 100644 sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-01/ses-022/sub-01_ses-022_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index f5c13dab4..6629739d5 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit f5c13dab41de8c7a7c801aacf9308c60d4531af7 +Subproject commit 6629739d5398fc91afd6b414d337a6259913dc72 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..4708c7800 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 46 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-022/anat/sub-01_ses-022_acq-axial_localizer.json b/sub-01/ses-022/anat/sub-01_ses-022_acq-axial_localizer.json new file mode 100644 index 000000000..db6e38acf --- /dev/null +++ b/sub-01/ses-022/anat/sub-01_ses-022_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:30:59.047500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0434341, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 599, + -7229, + -9119, + -10, + 50, + -38, + -82, + 55 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 284.4 +} \ No newline at end of file diff --git a/sub-01/ses-022/anat/sub-01_ses-022_acq-axial_localizer.nii.gz b/sub-01/ses-022/anat/sub-01_ses-022_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..b1763e856 --- /dev/null +++ b/sub-01/ses-022/anat/sub-01_ses-022_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Gw/zv/MD5E-s186400--1ab03334d0bdb0d96ac76bc635d2d3c4.nii.gz/MD5E-s186400--1ab03334d0bdb0d96ac76bc635d2d3c4.nii.gz \ No newline at end of file diff --git a/sub-01/ses-022/anat/sub-01_ses-022_acq-coronal_localizer.json b/sub-01/ses-022/anat/sub-01_ses-022_acq-coronal_localizer.json new file mode 100644 index 000000000..aa264347b --- /dev/null +++ b/sub-01/ses-022/anat/sub-01_ses-022_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:31:6.037500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0434341, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 599, + -7229, + -9119, + -10, + 50, + -38, + -82, + 55 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 284.4 +} \ No newline at end of file diff --git a/sub-01/ses-022/anat/sub-01_ses-022_acq-coronal_localizer.nii.gz b/sub-01/ses-022/anat/sub-01_ses-022_acq-coronal_localizer.nii.gz new file mode 120000 index 000000000..b3d3a97b5 --- /dev/null +++ b/sub-01/ses-022/anat/sub-01_ses-022_acq-coronal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/qk/w4/MD5E-s197888--7bc640703cd27290cef84ddd17100ddf.nii.gz/MD5E-s197888--7bc640703cd27290cef84ddd17100ddf.nii.gz \ No newline at end of file diff --git a/sub-01/ses-022/anat/sub-01_ses-022_acq-sagittal_localizer.json b/sub-01/ses-022/anat/sub-01_ses-022_acq-sagittal_localizer.json new file mode 100644 index 000000000..0f1cdef71 --- /dev/null +++ b/sub-01/ses-022/anat/sub-01_ses-022_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:30:52.057500", + "BaseResolution": 256, + 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a/sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-phase_sbref.json b/sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-phase_sbref.json new file mode 100644 index 000000000..833bba342 --- /dev/null +++ b/sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-phase_sbref.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:54:11.307500", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTime1": 0.037, + "EchoTime2": 0.001, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Single-band reference", + "ImageOrientationPatientDICOM": [ + 0.995908, + 0.0837967, + 0.033846, + -0.0682435, + 0.942825, + -0.326226 + ], + "ImageOrientationText": "Tra>Cor(-18.9)>Sag(3.4)", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "P", + "ND", + "MOSAIC", + "PHASE" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": 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a/sub-01/ses-022/sub-01_ses-022_scans.tsv b/sub-01/ses-022/sub-01_ses-022_scans.tsv new file mode 120000 index 000000000..3077f5ca1 --- /dev/null +++ b/sub-01/ses-022/sub-01_ses-022_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/5w/K8/MD5E-s2667--288bfa6cc1712b082cb02b57de90e491.tsv/MD5E-s2667--288bfa6cc1712b082cb02b57de90e491.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..14813f30d --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.995908, 0.0837967, 0.033846, -0.0682435, 0.942825, -0.326226], + "ImageOrientationText": "Tra>Cor(-18.9)>Sag(3.4)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0639742, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [609, -7232, -8785, 638, 135, -30, -73, 63], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 284.4, + "dcmmeta_affine": [ + [-1.9918158054351807, -0.13648700714111328, 0.11849506944417953, 109.96051025390625], + [-0.16759347915649414, 1.8856505155563354, -0.6451622843742371, -60.42102813720703], + [0.06769201159477234, 0.652451753616333, 1.8893715143203735, -57.60062789916992], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 1b570dd991d530ee23ee0ad98d1d8442296e9a77 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:13:46 -0400 Subject: [PATCH 072/463] fix fmap phase --- ...2_ses-003_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-003_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-003_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-02/ses-003/sub-02_ses-003_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-02/ses-003/fmap/{sub-02_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-003_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-003/fmap/{sub-02_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-003_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-003/fmap/sub-02_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-003/fmap/sub-02_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-003/fmap/{sub-02_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-003_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-003/fmap/{sub-02_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-003_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-003/fmap/{sub-02_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-003_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-003/fmap/{sub-02_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-003_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-003/fmap/{sub-02_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-003_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-003/fmap/{sub-02_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-003_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-003/fmap/{sub-02_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-003_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-003/fmap/{sub-02_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-003_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-003/fmap/sub-02_ses-003_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-003/fmap/sub-02_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-003/fmap/sub-02_ses-003_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-003/fmap/sub-02_ses-003_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-003/fmap/sub-02_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-003/fmap/sub-02_ses-003_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-003/fmap/sub-02_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 8e9779e7e..000000000 --- a/sub-02/ses-003/fmap/sub-02_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:20:4.075000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999198, -0.00676972, 0.0394533, 0.026863, 0.84411, -0.535497], - "ImageOrientationText": "Tra>Cor(-32.4)>Sag(1.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": 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sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index ce3ca631e..000000000 --- a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:19:53.645000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of 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b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 5ca3773c0..000000000 --- a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/6V/Ww/MD5E-s1112029--46da69bdeff7d6e0a417b17ba15ab929.nii.gz/MD5E-s1112029--46da69bdeff7d6e0a417b17ba15ab929.nii.gz \ No newline at end of file diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index e9c4cc3c2..000000000 --- a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:21:33.565000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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"PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0624453, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 632, - -7187, - -8870, - 249, - 58, - -245, - -58, - 31 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 287.299, - "WipMemBlock": "dfabfed9-297b-471b-91ca-d9a6739948c4||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 4033e45cb..000000000 --- a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/x1/0f/MD5E-s1103253--4a54d864d946fa868fc95bf50af4a335.nii.gz/MD5E-s1103253--4a54d864d946fa868fc95bf50af4a335.nii.gz \ No newline at end of file diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 51e78251d..000000000 --- a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:31:30.745000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999198, - -0.00676972, - 0.0394533, - 0.026863, - 0.84411, - -0.535497 - ], - "ImageOrientationText": "Tra>Cor(-32.4)>Sag(1.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0624453, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 632, - -7187, - -8870, - 249, - 58, - -245, - -58, - 31 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 287.299, - "WipMemBlock": "77b6d523-8b18-409e-b1b4-64cae8dcfb9b||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 37f37fdc0..000000000 --- a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Pv/mG/MD5E-s1103157--a5144fbfc6106687a2c9629a0bdaeeac.nii.gz/MD5E-s1103157--a5144fbfc6106687a2c9629a0bdaeeac.nii.gz \ No newline at end of file diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 95d6924d2..000000000 --- a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:41:12.995000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999198, - -0.00676972, - 0.0394533, - 0.026863, - 0.84411, - -0.535497 - ], - "ImageOrientationText": "Tra>Cor(-32.4)>Sag(1.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0624453, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 632, - -7187, - -8870, - 249, - 58, - -245, - -58, - 31 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 287.299, - "WipMemBlock": "876d34cf-f483-4fe4-ad96-2de2bf03a087||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index f2882de52..000000000 --- a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/fp/0P/MD5E-s1103286--339321e10e2672418255ed93b83819e8.nii.gz/MD5E-s1103286--339321e10e2672418255ed93b83819e8.nii.gz \ No newline at end of file diff --git a/sub-02/ses-003/sub-02_ses-003_scans.tsv b/sub-02/ses-003/sub-02_ses-003_scans.tsv index f65cb250b..e28204ba6 120000 --- a/sub-02/ses-003/sub-02_ses-003_scans.tsv +++ b/sub-02/ses-003/sub-02_ses-003_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/Xp/94/MD5E-s2667--9e330d653eeaa7501712227fb3998129.tsv/MD5E-s2667--9e330d653eeaa7501712227fb3998129.tsv \ No newline at end of file +../../.git/annex/objects/K1/wV/MD5E-s2066--da7fcb1336627f02447c48bcd374dae4.tsv/MD5E-s2066--da7fcb1336627f02447c48bcd374dae4.tsv \ No newline at end of file From 6c226efffdde7eae7f3076a891bd514802755582 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:13:52 -0400 Subject: [PATCH 073/463] fix complex event files --- ...g_events.tsv => sub-02_ses-003_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-02_ses-003_task-mario3_run-02_events.tsv} | 0 .../func/sub-02_ses-003_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-02_ses-003_task-mario3_run-03_events.tsv} | 0 .../func/sub-02_ses-003_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-02_ses-003_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-02/ses-003/func/{sub-02_ses-003_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-003_task-mario3_run-01_events.tsv} (100%) rename sub-02/ses-003/func/{sub-02_ses-003_task-mario3_run-01_part-phase_events.tsv => sub-02_ses-003_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-02_part-phase_events.tsv rename sub-02/ses-003/func/{sub-02_ses-003_task-mario3_run-02_part-mag_events.tsv => sub-02_ses-003_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-02_events.tsv similarity index 100% rename from sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-01_part-phase_events.tsv rename to sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-02_events.tsv diff --git a/sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-02_part-phase_events.tsv b/sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-02_part-mag_events.tsv b/sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_events.tsv similarity index 100% rename from sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-02_part-mag_events.tsv rename to sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_events.tsv diff --git a/sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_part-mag_events.tsv b/sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-003/func/sub-02_ses-003_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From cefd7dc30da367ac0884074ca4a62d95334e9c81 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:14:10 -0400 Subject: [PATCH 074/463] fix fmap phase --- ...1_ses-022_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-022_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-022_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-022_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-022_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-022_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-022_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-022_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-022_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-022_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-01/ses-022/sub-01_ses-022_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-01/ses-022/fmap/{sub-01_ses-022_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-022_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-022/fmap/{sub-01_ses-022_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-022_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-022/fmap/{sub-01_ses-022_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-022_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-022/fmap/{sub-01_ses-022_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-022_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-022/fmap/{sub-01_ses-022_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-022_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-022/fmap/{sub-01_ses-022_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-022_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-022/fmap/{sub-01_ses-022_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-022_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-022/fmap/{sub-01_ses-022_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-022_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-01/ses-022/fmap/{sub-01_ses-022_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-01_ses-022_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-01/ses-022/fmap/{sub-01_ses-022_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-01_ses-022_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 277d9c27e..000000000 --- a/sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:32:32.615000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - 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"TotalReadoutTime": 0.0576811, - "TxRefAmp": 284.4, - "WipMemBlock": "82b7fba1-b90c-4d19-ab4b-6e71a7a2b994||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9918158054351807, -0.13648700714111328, 0.11849506944417953, 109.96051025390625], - [-0.16759347915649414, 1.8856505155563354, -0.6451622843742371, -60.42102813720703], - [0.06769201159477234, 0.652451753616333, 1.8893715143203735, -57.60062789916992], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.9959079042997, 0.08379674319296, 0.03384600395359, -0.068243504988, 0.94282528060147, -0.3262258639129], - "ImagePositionPatient": [-771.24203427428, -881.18181139462, 222.45443855145], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.259296, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "113001.116000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.05101965892015, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "113319.638000", - "SliceLocation": -28.40891674995, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000158923, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "113000.746000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["113232.615000", "113234.105000", "113235.595000"], - "ContentTime": ["113319.640000", "113319.645000", "113319.648000"], - "InstanceCreationTime": ["113319.640000", "113319.645000", "113319.648000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4798.0, 4822.0, 4798.0], - "WindowWidth": [18610.0, 18642.0, 18606.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 0178bde97..000000000 --- a/sub-01/ses-022/fmap/sub-01_ses-022_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/03/ZW/MD5E-s3334855--4826fe7b5924eb7654c822a6c32134f7.nii.gz/MD5E-s3334855--4826fe7b5924eb7654c822a6c32134f7.nii.gz \ No newline at end of file diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 1f8845a4d..000000000 --- a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:32:22.185000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995908, - 0.0837967, - 0.033846, - -0.0682435, - 0.942825, - -0.326226 - ], - "ImageOrientationText": "Tra>Cor(-18.9)>Sag(3.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0510197, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 609, - -7232, - -8785, - 638, - 135, - -30, - -73, - 63 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 284.4, - "WipMemBlock": "82b7fba1-b90c-4d19-ab4b-6e71a7a2b994||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 50175e2d7..000000000 --- a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/fG/Q7/MD5E-s1112264--1e26967089ca5c4350ba677eb6be75f7.nii.gz/MD5E-s1112264--1e26967089ca5c4350ba677eb6be75f7.nii.gz \ No newline at end of file diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 6c3d2d33d..000000000 --- a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:33:32.845000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995908, - 0.0837967, - 0.033846, - -0.0682435, - 0.942825, - -0.326226 - ], - "ImageOrientationText": "Tra>Cor(-18.9)>Sag(3.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0639742, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 609, - -7232, - -8785, - 638, - 135, - -30, - -73, - 63 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 284.4, - "WipMemBlock": "a66ff378-9476-45f1-ab56-c66e1995dd9a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 4fb921304..000000000 --- a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/X2/GP/MD5E-s1103924--0004d1f94be45cce8d0b1bdb35e76aa2.nii.gz/MD5E-s1103924--0004d1f94be45cce8d0b1bdb35e76aa2.nii.gz \ No newline at end of file diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index fd2395ef8..000000000 --- a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:43:54.370000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995908, - 0.0837967, - 0.033846, - -0.0682435, - 0.942825, - -0.326226 - ], - "ImageOrientationText": "Tra>Cor(-18.9)>Sag(3.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0639742, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 609, - -7232, - -8785, - 638, - 135, - -30, - -73, - 63 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 284.4, - "WipMemBlock": "136ac0c3-f54a-4533-80af-bcecd5ef653c||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 53f487f43..000000000 --- a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/88/ZQ/MD5E-s1103872--ef8822ee2c7c53bb7e218dce685c1cf5.nii.gz/MD5E-s1103872--ef8822ee2c7c53bb7e218dce685c1cf5.nii.gz \ No newline at end of file diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 36f2f9876..000000000 --- a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:54:11.307500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995908, - 0.0837967, - 0.033846, - -0.0682435, - 0.942825, - -0.326226 - ], - "ImageOrientationText": "Tra>Cor(-18.9)>Sag(3.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0639742, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 609, - -7232, - -8785, - 638, - 135, - -30, - -73, - 63 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 284.4, - "WipMemBlock": "f4ea00e7-7c99-4a13-9c0b-d71d7c89b325||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index d844937f0..000000000 --- a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/x1/0w/MD5E-s1103929--9731ca45a76d35641aa0d1d96a070f27.nii.gz/MD5E-s1103929--9731ca45a76d35641aa0d1d96a070f27.nii.gz \ No newline at end of file diff --git a/sub-01/ses-022/sub-01_ses-022_scans.tsv b/sub-01/ses-022/sub-01_ses-022_scans.tsv index 3077f5ca1..03697624c 120000 --- a/sub-01/ses-022/sub-01_ses-022_scans.tsv +++ b/sub-01/ses-022/sub-01_ses-022_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/5w/K8/MD5E-s2667--288bfa6cc1712b082cb02b57de90e491.tsv/MD5E-s2667--288bfa6cc1712b082cb02b57de90e491.tsv \ No newline at end of file +../../.git/annex/objects/vM/Px/MD5E-s2066--5d0603ac83068399011a871c061073e5.tsv/MD5E-s2066--5d0603ac83068399011a871c061073e5.tsv \ No newline at end of file From d4a2119ed18d6d1263f66d34c9eb7b77426b8c03 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:14:17 -0400 Subject: [PATCH 075/463] fix complex event files --- ...g_events.tsv => sub-01_ses-022_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-022_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-022_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-01_ses-022_task-mario3_run-03_events.tsv} | 0 .../func/sub-01_ses-022_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-01_ses-022_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-01/ses-022/func/{sub-01_ses-022_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-022_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-022/func/{sub-01_ses-022_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-022_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-02_part-phase_events.tsv rename sub-01/ses-022/func/{sub-01_ses-022_task-mario3_run-02_part-mag_events.tsv => sub-01_ses-022_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_events.tsv similarity index 100% rename from sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-02_part-mag_events.tsv rename to sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_events.tsv diff --git a/sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-mag_events.tsv b/sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-022/func/sub-01_ses-022_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 001e11e0211a6a8fa6634c46286259f6fdb9e1b5 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:15:15 -0400 Subject: [PATCH 076/463] fill IntendedFor --- ...2_ses-003_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...2_ses-003_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...2_ses-003_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...2_ses-003_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_epi.json index 8ba1232ff..9211538cf 100644 --- a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999198, - -0.00676972, - 0.0394533, - 0.026863, - 0.84411, - -0.535497 - ], + "ImageOrientationPatientDICOM": [0.999198, -0.00676972, 0.0394533, 0.026863, 0.84411, -0.535497], "ImageOrientationText": "Tra>Cor(-32.4)>Sag(1.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-02_ses-003_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-003/func/sub-02_ses-003_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-003/func/sub-02_ses-003_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 632, - -7187, - -8870, - 249, - 58, - -245, - -58, - 31 - ], + "ShimSetting": [632, -7187, -8870, 249, 58, -245, -58, 31], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_epi.json b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_epi.json index 4086e3e4f..76690a8e6 100644 --- a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999198, - -0.00676972, - 0.0394533, - 0.026863, - 0.84411, - -0.535497 - ], + "ImageOrientationPatientDICOM": [0.999198, -0.00676972, 0.0394533, 0.026863, 0.84411, -0.535497], "ImageOrientationText": "Tra>Cor(-32.4)>Sag(1.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-02_ses-003_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 632, - -7187, - -8870, - 249, - 58, - -245, - -58, - 31 - ], + "ShimSetting": [632, -7187, -8870, 249, 58, -245, -58, 31], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_epi.json b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_epi.json index c97a328aa..fd99eb8c3 100644 --- a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999198, - -0.00676972, - 0.0394533, - 0.026863, - 0.84411, - -0.535497 - ], + "ImageOrientationPatientDICOM": [0.999198, -0.00676972, 0.0394533, 0.026863, 0.84411, -0.535497], "ImageOrientationText": "Tra>Cor(-32.4)>Sag(1.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-02_ses-003_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 632, - -7187, - -8870, - 249, - 58, - -245, - -58, - 31 - ], + "ShimSetting": [632, -7187, -8870, 249, 58, -245, -58, 31], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_epi.json b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_epi.json index 5b80975a1..3e575fe7b 100644 --- a/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-02/ses-003/fmap/sub-02_ses-003_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999198, - -0.00676972, - 0.0394533, - 0.026863, - 0.84411, - -0.535497 - ], + "ImageOrientationPatientDICOM": [0.999198, -0.00676972, 0.0394533, 0.026863, 0.84411, -0.535497], "ImageOrientationText": "Tra>Cor(-32.4)>Sag(1.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-02_ses-003_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 632, - -7187, - -8870, - 249, - 58, - -245, - -58, - 31 - ], + "ShimSetting": [632, -7187, -8870, 249, 58, -245, -58, 31], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From d4d32d3126e8b1a2f47e60497e6b391abeb73412 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:15:17 -0400 Subject: [PATCH 077/463] fill IntendedFor --- ...1_ses-022_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...1_ses-022_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-022_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...1_ses-022_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_epi.json index 3e1535214..2887a5209 100644 --- a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995908, - 0.0837967, - 0.033846, - -0.0682435, - 0.942825, - -0.326226 - ], + "ImageOrientationPatientDICOM": [0.995908, 0.0837967, 0.033846, -0.0682435, 0.942825, -0.326226], "ImageOrientationText": "Tra>Cor(-18.9)>Sag(3.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-022/func/sub-01_ses-022_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-022/func/sub-01_ses-022_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-022/func/sub-01_ses-022_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 609, - -7232, - -8785, - 638, - 135, - -30, - -73, - 63 - ], + "ShimSetting": [609, -7232, -8785, 638, 135, -30, -73, 63], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_epi.json index 9d70cd627..3f9771a51 100644 --- a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995908, - 0.0837967, - 0.033846, - -0.0682435, - 0.942825, - -0.326226 - ], + "ImageOrientationPatientDICOM": [0.995908, 0.0837967, 0.033846, -0.0682435, 0.942825, -0.326226], "ImageOrientationText": "Tra>Cor(-18.9)>Sag(3.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-022/func/sub-01_ses-022_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 609, - -7232, - -8785, - 638, - 135, - -30, - -73, - 63 - ], + "ShimSetting": [609, -7232, -8785, 638, 135, -30, -73, 63], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_epi.json index d15f14316..1417343a1 100644 --- a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995908, - 0.0837967, - 0.033846, - -0.0682435, - 0.942825, - -0.326226 - ], + "ImageOrientationPatientDICOM": [0.995908, 0.0837967, 0.033846, -0.0682435, 0.942825, -0.326226], "ImageOrientationText": "Tra>Cor(-18.9)>Sag(3.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-022/func/sub-01_ses-022_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 609, - -7232, - -8785, - 638, - 135, - -30, - -73, - 63 - ], + "ShimSetting": [609, -7232, -8785, 638, 135, -30, -73, 63], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_epi.json b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_epi.json index 5ba12dfc6..444e41136 100644 --- a/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-01/ses-022/fmap/sub-01_ses-022_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995908, - 0.0837967, - 0.033846, - -0.0682435, - 0.942825, - -0.326226 - ], + "ImageOrientationPatientDICOM": [0.995908, 0.0837967, 0.033846, -0.0682435, 0.942825, -0.326226], "ImageOrientationText": "Tra>Cor(-18.9)>Sag(3.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-022/func/sub-01_ses-022_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 609, - -7232, - -8785, - 638, - 135, - -30, - -73, - 63 - ], + "ShimSetting": [609, -7232, -8785, 638, 135, -30, -73, 63], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From fe01871c062d93a30a49c51cc86fea04fe452af4 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:16:18 -0400 Subject: [PATCH 078/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..9d35a9d10 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = f714eb8d-92de-44bf-a8e8-3dc52374aebd diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..33b6db9c6 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 33b6db9c6a1540bdcdc322ef0e4cbae8ba87d55c From 35baa4486a1569f0551fe25f199d50d452af3d6a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:17:00 -0400 Subject: [PATCH 079/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-012_acq-axial_localizer.json | 81 +++ .../sub-01_ses-012_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-012_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-012_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-012_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-012_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-012/anat/sub-01_ses-012_scout.json | 542 ++++++++++++++++++ .../ses-012/anat/sub-01_ses-012_scout.nii.gz | 1 + ...2_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-012_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...12_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...012_task-mario3_run-01_part-mag_events.tsv | 1 + ...012_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...12_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-01_part-phase_events.tsv | 1 + ...2_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-012_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...12_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...012_task-mario3_run-02_part-mag_events.tsv | 1 + ...012_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...12_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-02_part-phase_events.tsv | 1 + ...2_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-012_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...12_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...012_task-mario3_run-03_part-mag_events.tsv | 1 + ...012_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...12_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-03_part-phase_events.tsv | 1 + ...2_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-01/ses-012/sub-01_ses-012_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-012/anat/sub-01_ses-012_acq-axial_localizer.json create mode 120000 sub-01/ses-012/anat/sub-01_ses-012_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-012/anat/sub-01_ses-012_acq-coronal_localizer.json create mode 120000 sub-01/ses-012/anat/sub-01_ses-012_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-012/anat/sub-01_ses-012_acq-sagittal_localizer.json create mode 120000 sub-01/ses-012/anat/sub-01_ses-012_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-012/anat/sub-01_ses-012_scout.json create mode 120000 sub-01/ses-012/anat/sub-01_ses-012_scout.nii.gz create mode 100644 sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-03_part-mag_sbref.json create mode 120000 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-0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-012/anat/sub-01_ses-012_acq-axial_localizer.json b/sub-01/ses-012/anat/sub-01_ses-012_acq-axial_localizer.json new file mode 100644 index 000000000..c3aa66156 --- /dev/null +++ b/sub-01/ses-012/anat/sub-01_ses-012_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + 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a/sub-01/ses-012/anat/sub-01_ses-012_acq-axial_localizer.nii.gz b/sub-01/ses-012/anat/sub-01_ses-012_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..7b0fdd494 --- /dev/null +++ b/sub-01/ses-012/anat/sub-01_ses-012_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/WQ/9f/MD5E-s180818--73d2f463d549129f79f535e3b2f70d58.nii.gz/MD5E-s180818--73d2f463d549129f79f535e3b2f70d58.nii.gz \ No newline at end of file diff --git a/sub-01/ses-012/anat/sub-01_ses-012_acq-coronal_localizer.json b/sub-01/ses-012/anat/sub-01_ses-012_acq-coronal_localizer.json new file mode 100644 index 000000000..616f93413 --- /dev/null +++ b/sub-01/ses-012/anat/sub-01_ses-012_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:15:30.020000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + 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110.41600799560547], + [-0.17626775801181793, 1.8864659070968628, -0.6404499411582947, -63.15056228637695], + [0.06058883294463158, 0.6477307081222534, 1.8912360668182373, -66.97634887695312], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From d7f302152cd3d90eaf3989f81876c63ef3b529fa Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:17:34 -0400 Subject: [PATCH 080/463] fix fmap phase --- ...1_ses-012_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-012_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-012_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-012_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-012_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-012_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-012_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-012_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-012_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-012_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-01/ses-012/sub-01_ses-012_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-01/ses-012/fmap/{sub-01_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-012_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-012/fmap/{sub-01_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-012_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-012/fmap/{sub-01_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-012_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-012/fmap/{sub-01_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-012_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-012/fmap/{sub-01_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-012_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-012/fmap/{sub-01_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-012_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-012/fmap/{sub-01_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-012_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-012/fmap/{sub-01_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-012_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-01/ses-012/fmap/{sub-01_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-01_ses-012_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-01/ses-012/fmap/{sub-01_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-01_ses-012_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 09c5695b2..000000000 --- a/sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:16:24.895000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.995648, 0.0881339, 0.0302944, -0.07364, 0.943233, -0.323865], - "ImageOrientationText": "Tra>Cor(-18.7)>Sag(3.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 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"PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.05359082778084, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "181710.968000", - "SliceLocation": -36.804893137182, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000195549, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "181429.382000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["181624.895000", "181626.385000", "181627.875000"], - "ContentTime": ["181710.971000", "181710.973000", "181710.976000"], - "InstanceCreationTime": ["181710.971000", "181710.973000", "181710.976000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4798.0, 4804.0, 4826.0], - "WindowWidth": [18598.0, 18606.0, 18640.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 97ef8bda0..000000000 --- a/sub-01/ses-012/fmap/sub-01_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/6G/8G/MD5E-s3334708--f2939e24b1cd74233a1bbddb01384d6a.nii.gz/MD5E-s3334708--f2939e24b1cd74233a1bbddb01384d6a.nii.gz \ No newline at end of file diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 6f688a22d..000000000 --- a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:16:14.465000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995648, - 0.0881339, - 0.0302944, - -0.07364, - 0.943233, - -0.323865 - ], - "ImageOrientationText": "Tra>Cor(-18.7)>Sag(3.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0535908, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 622, - -7203, - -8824, - 661, - 134, - -5, - -48, - 7 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 280.397, - "WipMemBlock": "a07f1074-bd05-4372-aca0-5f538d7de9a9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 2719c8a19..000000000 --- a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/7j/Fk/MD5E-s1112327--fb0f0bec505e2ccc942fab0f93bbb0c5.nii.gz/MD5E-s1112327--fb0f0bec505e2ccc942fab0f93bbb0c5.nii.gz \ No newline at end of file diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index b70409486..000000000 --- a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:17:41.297500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995648, - 0.0881339, - 0.0302944, - -0.07364, - 0.943233, - -0.323865 - ], - "ImageOrientationText": "Tra>Cor(-18.7)>Sag(3.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0671982, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 622, - -7203, - -8824, - 661, - 134, - -5, - -48, - 7 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 280.397, - "WipMemBlock": "af114602-bb98-4dc7-8279-ae04ea97edd0||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index c3320ed17..000000000 --- a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/65/Q6/MD5E-s1103954--c93cbb81d603e5297d7e8e25c4be34dc.nii.gz/MD5E-s1103954--c93cbb81d603e5297d7e8e25c4be34dc.nii.gz \ No newline at end of file diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index fb6962bb4..000000000 --- a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:29:42.275000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995648, - 0.0881339, - 0.0302944, - -0.07364, - 0.943233, - -0.323865 - ], - "ImageOrientationText": "Tra>Cor(-18.7)>Sag(3.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0671982, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 622, - -7203, - -8824, - 661, - 134, - -5, - -48, - 7 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 280.397, - "WipMemBlock": "a6a01692-37b8-4cdb-9c61-c6d08a096ff8||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 685186863..000000000 --- a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/GP/kZ/MD5E-s1103697--d71235e9fb6637eb4ed631a1b405bfc3.nii.gz/MD5E-s1103697--d71235e9fb6637eb4ed631a1b405bfc3.nii.gz \ No newline at end of file diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 3b88f580d..000000000 --- a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:41:37.632500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995648, - 0.0881339, - 0.0302944, - -0.07364, - 0.943233, - -0.323865 - ], - "ImageOrientationText": "Tra>Cor(-18.7)>Sag(3.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0671982, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 622, - -7203, - -8824, - 661, - 134, - -5, - -48, - 7 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 280.397, - "WipMemBlock": "7b1a4fce-a23c-4183-9314-4fa28a4101ae||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 87d4b36ae..000000000 --- a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/jG/x9/MD5E-s1103841--db74195b73f642e451bd54a70a57a72d.nii.gz/MD5E-s1103841--db74195b73f642e451bd54a70a57a72d.nii.gz \ No newline at end of file diff --git a/sub-01/ses-012/sub-01_ses-012_scans.tsv b/sub-01/ses-012/sub-01_ses-012_scans.tsv index 33dd6fc0d..1414dc78f 120000 --- a/sub-01/ses-012/sub-01_ses-012_scans.tsv +++ b/sub-01/ses-012/sub-01_ses-012_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/jz/f6/MD5E-s2667--13953fb5043b0a0668f4583576130efe.tsv/MD5E-s2667--13953fb5043b0a0668f4583576130efe.tsv \ No newline at end of file +../../.git/annex/objects/v2/w5/MD5E-s2066--6111dcad6a1ece8881c25beeb8b27505.tsv/MD5E-s2066--6111dcad6a1ece8881c25beeb8b27505.tsv \ No newline at end of file From 8a824074eeac5bd96e03ec6b9f768bacb50b08ee Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:17:42 -0400 Subject: [PATCH 081/463] fix complex event files --- ...g_events.tsv => sub-01_ses-012_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-012_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-012_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-01_ses-012_task-mario3_run-03_events.tsv} | 0 .../func/sub-01_ses-012_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-01_ses-012_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-01/ses-012/func/{sub-01_ses-012_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-012_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-012/func/{sub-01_ses-012_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-012_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-02_part-phase_events.tsv rename sub-01/ses-012/func/{sub-01_ses-012_task-mario3_run-02_part-mag_events.tsv => sub-01_ses-012_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-03_events.tsv similarity index 100% rename from sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-02_part-mag_events.tsv rename to sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-03_events.tsv diff --git a/sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-03_part-mag_events.tsv b/sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-012/func/sub-01_ses-012_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 4251fed1ca32de620bfc34e188c23e367fd84395 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:17:44 -0400 Subject: [PATCH 082/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..ea7db1f33 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 9021d9a8-a796-46b1-842a-28577cf51883 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..9f0ff2a09 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 9f0ff2a0972f03e0ffa144b8b7d8a7fb2507d606 From 95451ff429fbab27f029a8b8c77f2704dbde1513 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:17:56 -0400 Subject: [PATCH 083/463] fill IntendedFor --- ...1_ses-012_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...1_ses-012_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-012_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...1_ses-012_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_epi.json index 97f57b9ae..a5016ef3b 100644 --- a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995648, - 0.0881339, - 0.0302944, - -0.07364, - 0.943233, - -0.323865 - ], + "ImageOrientationPatientDICOM": [0.995648, 0.0881339, 0.0302944, -0.07364, 0.943233, -0.323865], "ImageOrientationText": "Tra>Cor(-18.7)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-012/func/sub-01_ses-012_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-012/func/sub-01_ses-012_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-012/func/sub-01_ses-012_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 622, - -7203, - -8824, - 661, - 134, - -5, - -48, - 7 - ], + "ShimSetting": [622, -7203, -8824, 661, 134, -5, -48, 7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_epi.json index 902e16208..6a77f78f0 100644 --- a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995648, - 0.0881339, - 0.0302944, - -0.07364, - 0.943233, - -0.323865 - ], + "ImageOrientationPatientDICOM": [0.995648, 0.0881339, 0.0302944, -0.07364, 0.943233, -0.323865], "ImageOrientationText": "Tra>Cor(-18.7)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-012/func/sub-01_ses-012_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 622, - -7203, - -8824, - 661, - 134, - -5, - -48, - 7 - ], + "ShimSetting": [622, -7203, -8824, 661, 134, -5, -48, 7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_epi.json index 302016af4..6d8727df8 100644 --- a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995648, - 0.0881339, - 0.0302944, - -0.07364, - 0.943233, - -0.323865 - ], + "ImageOrientationPatientDICOM": [0.995648, 0.0881339, 0.0302944, -0.07364, 0.943233, -0.323865], "ImageOrientationText": "Tra>Cor(-18.7)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-012/func/sub-01_ses-012_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 622, - -7203, - -8824, - 661, - 134, - -5, - -48, - 7 - ], + "ShimSetting": [622, -7203, -8824, 661, 134, -5, -48, 7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_epi.json b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_epi.json index 7b43ca270..122ed45c1 100644 --- a/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-01/ses-012/fmap/sub-01_ses-012_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995648, - 0.0881339, - 0.0302944, - -0.07364, - 0.943233, - -0.323865 - ], + "ImageOrientationPatientDICOM": [0.995648, 0.0881339, 0.0302944, -0.07364, 0.943233, -0.323865], "ImageOrientationText": "Tra>Cor(-18.7)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-012/func/sub-01_ses-012_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 622, - -7203, - -8824, - 661, - 134, - -5, - -48, - 7 - ], + "ShimSetting": [622, -7203, -8824, 661, 134, -5, -48, 7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 112eea32441c378a3f0c915ddec21c316eabe482 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:17:57 -0400 Subject: [PATCH 084/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..668240790 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = f598c505-b0ee-4b0a-adc4-0e7c17e4a2d8 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..7532dce19 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 7532dce194be3ca1b010a1e011ee2c02884488e3 From 2663b19bbf888d48c19aeb43b284401c283346df Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:18:52 -0400 Subject: [PATCH 085/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..e8c5b6482 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = c2ecf5cb-89cc-4b5a-9b25-cfb958aa5df1 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..784335139 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 784335139e59c3ee01bec27397501a01a596d752 From b7f1e7775f14fc2efb565270d98ffdafeb9cafa8 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:22:07 -0400 Subject: [PATCH 086/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-005_acq-axial_localizer.json | 81 +++ .../sub-02_ses-005_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-005_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-005_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-005_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-005_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-005/anat/sub-02_ses-005_scout.json | 542 ++++++++++++++++++ .../ses-005/anat/sub-02_ses-005_scout.nii.gz | 1 + ...5_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-005_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...05_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...005_task-mario3_run-01_part-mag_events.tsv | 1 + ...005_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...05_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-01_part-phase_events.tsv | 1 + ...5_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-005_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...05_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...005_task-mario3_run-02_part-mag_events.tsv | 1 + ...005_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...05_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-02_part-phase_events.tsv | 1 + ...5_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-005_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...05_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...005_task-mario3_run-03_part-mag_events.tsv | 1 + ...005_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...05_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-03_part-phase_events.tsv | 1 + ...5_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-02/ses-005/sub-02_ses-005_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-005/anat/sub-02_ses-005_acq-axial_localizer.json create mode 120000 sub-02/ses-005/anat/sub-02_ses-005_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-005/anat/sub-02_ses-005_acq-coronal_localizer.json create mode 120000 sub-02/ses-005/anat/sub-02_ses-005_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-005/anat/sub-02_ses-005_acq-sagittal_localizer.json create mode 120000 sub-02/ses-005/anat/sub-02_ses-005_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-005/anat/sub-02_ses-005_scout.json create mode 120000 sub-02/ses-005/anat/sub-02_ses-005_scout.nii.gz create mode 100644 sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-02/ses-005/sub-02_ses-005_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 48279dba9..e1cbab483 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 48279dba905c498b0895be513dc43398e5792da4 +Subproject commit e1cbab48358c879bcf30b14fc672d2c605397f0d diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..83ada7a9d --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 51 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-005/anat/sub-02_ses-005_acq-axial_localizer.json b/sub-02/ses-005/anat/sub-02_ses-005_acq-axial_localizer.json new file mode 100644 index 000000000..b0ace77f5 --- /dev/null +++ b/sub-02/ses-005/anat/sub-02_ses-005_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:25:50.067500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0650522, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 321.071 +} \ No newline at end of file diff --git a/sub-02/ses-005/anat/sub-02_ses-005_acq-axial_localizer.nii.gz b/sub-02/ses-005/anat/sub-02_ses-005_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..2371f4da5 --- /dev/null +++ b/sub-02/ses-005/anat/sub-02_ses-005_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/V4/xZ/MD5E-s183843--a00b362eb087736955d11f55ca5be04a.nii.gz/MD5E-s183843--a00b362eb087736955d11f55ca5be04a.nii.gz \ No newline at end of file diff --git a/sub-02/ses-005/anat/sub-02_ses-005_acq-coronal_localizer.json b/sub-02/ses-005/anat/sub-02_ses-005_acq-coronal_localizer.json new file mode 100644 index 000000000..9f3127f35 --- /dev/null +++ b/sub-02/ses-005/anat/sub-02_ses-005_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:25:57.057500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0650522, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": 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"PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0958155, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [628, -7193, -8870, 224, 50, -216, -39, 58], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 321.071, + "dcmmeta_affine": [ + [-1.9973804950714111, 0.0446292906999588, 0.09208263456821442, 102.88335418701172], + [-0.01265551708638668, 1.6782008409500122, -1.0878794193267822, -46.65126419067383], + [0.10154221951961517, 1.087037205696106, 1.6757205724716187, -95.35989379882812], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From ba1ee8f205b9b4e10109d5e1f8f991500a922860 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:22:38 -0400 Subject: [PATCH 087/463] fix fmap phase --- ...2_ses-005_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-005_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-005_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-005_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-005_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-005_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-02/ses-005/sub-02_ses-005_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-02/ses-005/fmap/{sub-02_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-005_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-005/fmap/{sub-02_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-005_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-005/fmap/{sub-02_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-005_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-005/fmap/{sub-02_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-005_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-005/fmap/{sub-02_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-005_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-005/fmap/{sub-02_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-005_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-005/fmap/{sub-02_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-005_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-005/fmap/{sub-02_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-005_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-005/fmap/{sub-02_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-005_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-005/fmap/{sub-02_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-005_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 558525efa..000000000 --- a/sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:26:52.990000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.99869, 0.00632776, 0.0507711, 0.0223146, 0.8391, -0.543519], - "ImageOrientationText": "Tra>Cor(-33.0)>Sag(2.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0764132, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [628, -7193, -8870, 224, 50, -216, -39, 58], - "SliceThickness": 2, - "SliceTiming": [0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 321.071, - "WipMemBlock": "bbcffa16-337c-4e66-a456-0f1a7ec7b74a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9973804950714111, 0.0446292906999588, 0.09208263456821442, 102.88335418701172], - [-0.01265551708638668, 1.6782008409500122, -1.0878794193267822, -46.65126419067383], - [0.10154221951961517, 1.087037205696106, 1.6757205724716187, -95.35989379882812], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99869026926487, 0.00632775836548, 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0.07641322624709, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "162739.360000", - "SliceLocation": -49.785904022897, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000343028, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "162500.245000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["162652.990000", "162654.480000", "162655.970000"], - "ContentTime": ["162739.363000", "162739.366000", "162739.368000"], - "InstanceCreationTime": ["162739.363000", "162739.366000", "162739.368000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4902.0, 4908.0, 4896.0], - "WindowWidth": [18702.0, 18694.0, 18704.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 080bdc50a..000000000 --- a/sub-02/ses-005/fmap/sub-02_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/vm/K4/MD5E-s3333435--30f5a742c5b79513b8297a10a27e00ba.nii.gz/MD5E-s3333435--30f5a742c5b79513b8297a10a27e00ba.nii.gz \ No newline at end of file diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 70327ce87..000000000 --- a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:26:42.560000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99869, - 0.00632776, - 0.0507711, - 0.0223146, - 0.8391, - -0.543519 - ], - "ImageOrientationText": "Tra>Cor(-33.0)>Sag(2.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0764132, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 628, - -7193, - -8870, - 224, - 50, - -216, - -39, - 58 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 321.071, - "WipMemBlock": "bbcffa16-337c-4e66-a456-0f1a7ec7b74a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 674e53abc..000000000 --- a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Qz/m7/MD5E-s1112088--6d6a19448eae8a62d7780cbeab18f1e5.nii.gz/MD5E-s1112088--6d6a19448eae8a62d7780cbeab18f1e5.nii.gz \ No newline at end of file diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 4f323c042..000000000 --- a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:28:8.262500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99869, - 0.00632776, - 0.0507711, - 0.0223146, - 0.8391, - -0.543519 - ], - "ImageOrientationText": "Tra>Cor(-33.0)>Sag(2.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0958155, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 628, - -7193, - -8870, - 224, - 50, - -216, - -39, - 58 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 321.071, - "WipMemBlock": "d5784be4-4700-4642-b18d-d00a2116952f||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index fecefea93..000000000 --- a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/49/wQ/MD5E-s1103246--3df3c92da5b36c5076d592c4de7837d2.nii.gz/MD5E-s1103246--3df3c92da5b36c5076d592c4de7837d2.nii.gz \ No newline at end of file diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 95cfe1108..000000000 --- a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:38:43.982500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99869, - 0.00632776, - 0.0507711, - 0.0223146, - 0.8391, - -0.543519 - ], - "ImageOrientationText": "Tra>Cor(-33.0)>Sag(2.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0958155, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 628, - -7193, - -8870, - 224, - 50, - -216, - -39, - 58 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 321.071, - "WipMemBlock": "f1fc65e8-0691-46d7-acb6-7455c85f0cdd||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 09f17d6c0..000000000 --- a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/6X/mX/MD5E-s1103342--542d8f1bb38433f64d060208c2a22777.nii.gz/MD5E-s1103342--542d8f1bb38433f64d060208c2a22777.nii.gz \ No newline at end of file diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 9ff96868f..000000000 --- a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:51:10.027500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99869, - 0.00632776, - 0.0507711, - 0.0223146, - 0.8391, - -0.543519 - ], - "ImageOrientationText": "Tra>Cor(-33.0)>Sag(2.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0958155, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 628, - -7193, - -8870, - 224, - 50, - -216, - -39, - 58 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 321.071, - "WipMemBlock": "b69d67e6-6dcd-44fa-8a88-634ec215c66c||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 659aa5ddb..000000000 --- a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/QJ/ZW/MD5E-s1103260--f79ff2642ba44c15234986cd0ebd8ace.nii.gz/MD5E-s1103260--f79ff2642ba44c15234986cd0ebd8ace.nii.gz \ No newline at end of file diff --git a/sub-02/ses-005/sub-02_ses-005_scans.tsv b/sub-02/ses-005/sub-02_ses-005_scans.tsv index 9781c2cbc..6792eb5fb 120000 --- a/sub-02/ses-005/sub-02_ses-005_scans.tsv +++ b/sub-02/ses-005/sub-02_ses-005_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/kv/9q/MD5E-s2667--b680c61f6ceb0a99f784e70f7eb3a0f5.tsv/MD5E-s2667--b680c61f6ceb0a99f784e70f7eb3a0f5.tsv \ No newline at end of file +../../.git/annex/objects/jq/VV/MD5E-s2066--08f2b4aef88fc20b9fdfba7cdcdb36d3.tsv/MD5E-s2066--08f2b4aef88fc20b9fdfba7cdcdb36d3.tsv \ No newline at end of file From c6d00b01b9db4e3f5299a3c880d0cd5792972156 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:22:45 -0400 Subject: [PATCH 088/463] fix complex event files --- ...g_events.tsv => sub-02_ses-005_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-02_ses-005_task-mario3_run-02_events.tsv} | 0 .../func/sub-02_ses-005_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-02_ses-005_task-mario3_run-03_events.tsv} | 0 .../func/sub-02_ses-005_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-02_ses-005_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-02/ses-005/func/{sub-02_ses-005_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-005_task-mario3_run-01_events.tsv} (100%) rename sub-02/ses-005/func/{sub-02_ses-005_task-mario3_run-01_part-phase_events.tsv => sub-02_ses-005_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_part-phase_events.tsv rename sub-02/ses-005/func/{sub-02_ses-005_task-mario3_run-02_part-mag_events.tsv => sub-02_ses-005_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_events.tsv similarity index 100% rename from sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-01_part-phase_events.tsv rename to sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_events.tsv diff --git a/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_part-phase_events.tsv b/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_part-mag_events.tsv b/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_events.tsv similarity index 100% rename from sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_part-mag_events.tsv rename to sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_events.tsv diff --git a/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_part-mag_events.tsv b/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 6683834b2c163c777d53d2d7bc4ebb137123032e Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:24:10 -0400 Subject: [PATCH 089/463] fill IntendedFor --- ...2_ses-005_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...2_ses-005_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...2_ses-005_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...2_ses-005_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_epi.json index 7981fb17b..89bbd8e39 100644 --- a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99869, - 0.00632776, - 0.0507711, - 0.0223146, - 0.8391, - -0.543519 - ], + "ImageOrientationPatientDICOM": [0.99869, 0.00632776, 0.0507711, 0.0223146, 0.8391, -0.543519], "ImageOrientationText": "Tra>Cor(-33.0)>Sag(2.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-02_ses-005_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-005/func/sub-02_ses-005_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-005/func/sub-02_ses-005_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 628, - -7193, - -8870, - 224, - 50, - -216, - -39, - 58 - ], + "ShimSetting": [628, -7193, -8870, 224, 50, -216, -39, 58], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_epi.json b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_epi.json index 70050f5d8..4e44d544d 100644 --- a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99869, - 0.00632776, - 0.0507711, - 0.0223146, - 0.8391, - -0.543519 - ], + "ImageOrientationPatientDICOM": [0.99869, 0.00632776, 0.0507711, 0.0223146, 0.8391, -0.543519], "ImageOrientationText": "Tra>Cor(-33.0)>Sag(2.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-02_ses-005_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 628, - -7193, - -8870, - 224, - 50, - -216, - -39, - 58 - ], + "ShimSetting": [628, -7193, -8870, 224, 50, -216, -39, 58], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_epi.json b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_epi.json index f496e2237..d99349e53 100644 --- a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99869, - 0.00632776, - 0.0507711, - 0.0223146, - 0.8391, - -0.543519 - ], + "ImageOrientationPatientDICOM": [0.99869, 0.00632776, 0.0507711, 0.0223146, 0.8391, -0.543519], "ImageOrientationText": "Tra>Cor(-33.0)>Sag(2.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-02_ses-005_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 628, - -7193, - -8870, - 224, - 50, - -216, - -39, - 58 - ], + "ShimSetting": [628, -7193, -8870, 224, 50, -216, -39, 58], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_epi.json b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_epi.json index 7ad4f015f..9f403faef 100644 --- a/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-02/ses-005/fmap/sub-02_ses-005_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99869, - 0.00632776, - 0.0507711, - 0.0223146, - 0.8391, - -0.543519 - ], + "ImageOrientationPatientDICOM": [0.99869, 0.00632776, 0.0507711, 0.0223146, 0.8391, -0.543519], "ImageOrientationText": "Tra>Cor(-33.0)>Sag(2.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-02_ses-005_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 628, - -7193, - -8870, - 224, - 50, - -216, - -39, - 58 - ], + "ShimSetting": [628, -7193, -8870, 224, 50, -216, -39, 58], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 68f52343a267b9ac0a79ea4a8aaea1cdea5dd24a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:25:08 -0400 Subject: [PATCH 090/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..a7369232b --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 60e890da-5c2b-4292-aba7-cdcc757d229c diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..def1d1689 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit def1d1689d1cc283b8bab71f366ed9dec2d094b1 From d639700d2812f6faf90125c36a3df1cea39b9272 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:28:46 -0400 Subject: [PATCH 091/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..22ad118fa --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 9c4f61ed-8721-4113-8573-c22b651c2c2e diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..b90c06fee --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit b90c06fee70f2b7f20ce48f1f9612f19456d5a55 From e05e8477c01104d58ddb63645acdb9f0f2560654 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:30:12 -0400 Subject: [PATCH 092/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..70771ce48 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = a5c304c2-cf4f-49cb-a191-8a792710dc92 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..d7a47ae21 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit d7a47ae21e971dc044006156fa5ef9fa76d1e182 From e0755cf940437e63077e2dca5ff61f6ca25fcfa5 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:31:00 -0400 Subject: [PATCH 093/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..b7b6757ec --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 271134c2-68a7-416b-b11e-c7d4ad43e0ae diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..a3aa96342 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit a3aa96342fb12f7e33e68b0b716ea06c8f3bb422 From 323f854f620b8de70a779e260b66c9f4b61682b5 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:31:24 -0400 Subject: [PATCH 094/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-004_acq-axial_localizer.json | 81 +++ .../sub-02_ses-004_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-004_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-004_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-004_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-004_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-004/anat/sub-02_ses-004_scout.json | 542 ++++++++++++++++++ .../ses-004/anat/sub-02_ses-004_scout.nii.gz | 1 + ...4_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-004_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...04_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...004_task-mario3_run-01_part-mag_events.tsv | 1 + ...004_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...04_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-01_part-phase_events.tsv | 1 + ...4_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-004_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...04_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...004_task-mario3_run-02_part-mag_events.tsv | 1 + ...004_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...04_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-02_part-phase_events.tsv | 1 + ...4_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-004_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...04_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...004_task-mario3_run-03_part-mag_events.tsv | 1 + ...004_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...04_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-03_part-phase_events.tsv | 1 + ...4_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-02/ses-004/sub-02_ses-004_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-004/anat/sub-02_ses-004_acq-axial_localizer.json create mode 120000 sub-02/ses-004/anat/sub-02_ses-004_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-004/anat/sub-02_ses-004_acq-coronal_localizer.json create mode 120000 sub-02/ses-004/anat/sub-02_ses-004_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-004/anat/sub-02_ses-004_acq-sagittal_localizer.json create mode 120000 sub-02/ses-004/anat/sub-02_ses-004_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-004/anat/sub-02_ses-004_scout.json create mode 120000 sub-02/ses-004/anat/sub-02_ses-004_scout.nii.gz create mode 100644 sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-02/ses-004/sub-02_ses-004_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index a3aa96342..0ac4f4287 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit a3aa96342fb12f7e33e68b0b716ea06c8f3bb422 +Subproject commit 0ac4f4287f0800ab07a76c5fad9d08fefe3a9221 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..83ada7a9d --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 51 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-004/anat/sub-02_ses-004_acq-axial_localizer.json b/sub-02/ses-004/anat/sub-02_ses-004_acq-axial_localizer.json new file mode 100644 index 000000000..a9472fa6b --- /dev/null +++ b/sub-02/ses-004/anat/sub-02_ses-004_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:21:44.067500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0380568, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": 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"slices": {} + } +} \ No newline at end of file diff --git a/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-phase_bold.nii.gz b/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-phase_bold.nii.gz new file mode 120000 index 000000000..6c9b3037c --- /dev/null +++ b/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-phase_bold.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/P4/Q4/MD5E-s416670720--09c26534ea7e47ab672eec212cd4d806.nii.gz/MD5E-s416670720--09c26534ea7e47ab672eec212cd4d806.nii.gz \ No newline at end of file diff --git a/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-phase_events.tsv new file mode 120000 index 000000000..1bbdfddb5 --- /dev/null +++ b/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-phase_events.tsv @@ -0,0 +1 @@ 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"N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999348, 0.0113317, 0.0342759, 0.00889558, 0.842886, -0.538019], + "ImageOrientationText": "Tra>Cor(-32.6)>Sag(2.0)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + 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104.50016021728516], + [-0.02266332507133484, 1.6857718229293823, -1.0759458541870117, -46.75326156616211], + [0.06855180859565735, 1.0760375261306763, 1.6844713687896729, -96.80511474609375], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 59090e0fcaebb0fb5052f8e74c5459fd8007c0f5 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:31:57 -0400 Subject: [PATCH 095/463] fix fmap phase --- ...2_ses-004_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-004_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-004_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-004_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-004_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-004_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-02/ses-004/sub-02_ses-004_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-02/ses-004/fmap/{sub-02_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-004_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-004/fmap/{sub-02_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-004_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-004/fmap/{sub-02_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-004_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-004/fmap/{sub-02_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-004_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-004/fmap/{sub-02_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-004_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-004/fmap/{sub-02_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-004_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-004/fmap/{sub-02_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-004_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-004/fmap/{sub-02_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-004_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-004/fmap/{sub-02_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-004_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-004/fmap/{sub-02_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-004_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 840e8461e..000000000 --- a/sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:22:46.735000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - 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"PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0447032, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [625, -7183, -8879, 232, 8, -217, 1, 26], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.0975, 0.8825, 0.195, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685, 0, 0.785, 0.0975, 0.8825, 0.195, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685, 0, 0.785, 0.0975, 0.8825, 0.195, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685, 0, 0.785, 0.0975, 0.8825, 0.195, 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["112246.735000", "112248.225000", "112249.715000"], - "ContentTime": ["112333.674000", "112333.677000", "112333.680000"], - "InstanceCreationTime": ["112333.674000", "112333.677000", "112333.680000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4930.0, 4894.0, 4904.0], - "WindowWidth": [18732.0, 18720.0, 18706.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index eb8a1a0d9..000000000 --- a/sub-02/ses-004/fmap/sub-02_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/0w/fZ/MD5E-s3333243--086b0f28b56e5d17780f720e794eec2c.nii.gz/MD5E-s3333243--086b0f28b56e5d17780f720e794eec2c.nii.gz \ No newline at end of file diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 6e9217a40..000000000 --- a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:22:36.305000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999348, - 0.0113317, - 0.0342759, - 0.00889558, - 0.842886, - -0.538019 - ], - "ImageOrientationText": "Tra>Cor(-32.6)>Sag(2.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0447032, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 625, - -7183, - -8879, - 232, - 8, - -217, - 1, - 26 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 275.739, - "WipMemBlock": "09f4ab3a-a492-4a72-9f39-8dd8eef4ae6b||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 4af50a194..000000000 --- a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/p1/Qz/MD5E-s1111994--6b35d6b7d059231823aceb73b8f86218.nii.gz/MD5E-s1111994--6b35d6b7d059231823aceb73b8f86218.nii.gz \ No newline at end of file diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 8ba8cba1f..000000000 --- a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:27:27.257500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999348, - 0.0113317, - 0.0342759, - 0.00889558, - 0.842886, - -0.538019 - ], - "ImageOrientationText": "Tra>Cor(-32.6)>Sag(2.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0560539, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 625, - -7183, - -8879, - 232, - 8, - -217, - 1, - 26 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 275.739, - "WipMemBlock": "1b7f879d-c3e3-4faa-92b5-d64cb741c305||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 0a8d9851a..000000000 --- a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/q4/69/MD5E-s1103337--f8cc9e54c90e3721d4e7f5336c04c386.nii.gz/MD5E-s1103337--f8cc9e54c90e3721d4e7f5336c04c386.nii.gz \ No newline at end of file diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index cb1749ff5..000000000 --- a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:37:57.810000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999348, - 0.0113317, - 0.0342759, - 0.00889558, - 0.842886, - -0.538019 - ], - "ImageOrientationText": "Tra>Cor(-32.6)>Sag(2.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0560539, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 625, - -7183, - -8879, - 232, - 8, - -217, - 1, - 26 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 275.739, - "WipMemBlock": "4ae2897e-d921-4223-8195-e239ba45da13||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index eb11d5a09..000000000 --- a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/0G/xX/MD5E-s1103459--a0eb3ea7fd0ade331f0a47278d4dee33.nii.gz/MD5E-s1103459--a0eb3ea7fd0ade331f0a47278d4dee33.nii.gz \ No newline at end of file diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 09d3b2d2e..000000000 --- a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:46:52.577500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999348, - 0.0113317, - 0.0342759, - 0.00889558, - 0.842886, - -0.538019 - ], - "ImageOrientationText": "Tra>Cor(-32.6)>Sag(2.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0560539, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 625, - -7183, - -8879, - 232, - 8, - -217, - 1, - 26 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 275.739, - "WipMemBlock": "19213869-a442-43d3-ba98-331b19f93922||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 9bc4737bb..000000000 --- a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/5Z/vJ/MD5E-s1103497--9b26b1a2c0c2f60d67b842f41c925fae.nii.gz/MD5E-s1103497--9b26b1a2c0c2f60d67b842f41c925fae.nii.gz \ No newline at end of file diff --git a/sub-02/ses-004/sub-02_ses-004_scans.tsv b/sub-02/ses-004/sub-02_ses-004_scans.tsv index 61952b24c..9fd407bb2 120000 --- a/sub-02/ses-004/sub-02_ses-004_scans.tsv +++ b/sub-02/ses-004/sub-02_ses-004_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/57/4q/MD5E-s2667--dd93e0c5026d554061c529b048502c14.tsv/MD5E-s2667--dd93e0c5026d554061c529b048502c14.tsv \ No newline at end of file +../../.git/annex/objects/5m/f6/MD5E-s2066--a945f072e536a690513f66e3bb86d264.tsv/MD5E-s2066--a945f072e536a690513f66e3bb86d264.tsv \ No newline at end of file From 338c514b68683500b7cec8aba12f95a57fe4b588 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:32:05 -0400 Subject: [PATCH 096/463] fix complex event files --- ...g_events.tsv => sub-02_ses-004_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-02_ses-004_task-mario3_run-02_events.tsv} | 0 .../func/sub-02_ses-004_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-02_ses-004_task-mario3_run-03_events.tsv} | 0 .../func/sub-02_ses-004_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-02_ses-004_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-02/ses-004/func/{sub-02_ses-004_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-004_task-mario3_run-01_events.tsv} (100%) rename sub-02/ses-004/func/{sub-02_ses-004_task-mario3_run-01_part-phase_events.tsv => sub-02_ses-004_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-02_part-phase_events.tsv rename sub-02/ses-004/func/{sub-02_ses-004_task-mario3_run-02_part-mag_events.tsv => sub-02_ses-004_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-02_events.tsv similarity index 100% rename from sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-01_part-phase_events.tsv rename to sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-02_events.tsv diff --git a/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-02_part-phase_events.tsv b/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-02_part-mag_events.tsv b/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_events.tsv similarity index 100% rename from sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-02_part-mag_events.tsv rename to sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_events.tsv diff --git a/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-mag_events.tsv b/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-004/func/sub-02_ses-004_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From f20b1f29cb868776447773137172866a56e64979 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:33:04 -0400 Subject: [PATCH 097/463] fill IntendedFor --- ...2_ses-004_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...2_ses-004_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...2_ses-004_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...2_ses-004_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_epi.json index fbe452df3..273cef2fa 100644 --- a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999348, - 0.0113317, - 0.0342759, - 0.00889558, - 0.842886, - -0.538019 - ], + "ImageOrientationPatientDICOM": [0.999348, 0.0113317, 0.0342759, 0.00889558, 0.842886, -0.538019], "ImageOrientationText": "Tra>Cor(-32.6)>Sag(2.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-02_ses-004_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-004/func/sub-02_ses-004_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-004/func/sub-02_ses-004_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 625, - -7183, - -8879, - 232, - 8, - -217, - 1, - 26 - ], + "ShimSetting": [625, -7183, -8879, 232, 8, -217, 1, 26], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_epi.json b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_epi.json index 9c3d9fcea..8b1dd0d20 100644 --- a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999348, - 0.0113317, - 0.0342759, - 0.00889558, - 0.842886, - -0.538019 - ], + "ImageOrientationPatientDICOM": [0.999348, 0.0113317, 0.0342759, 0.00889558, 0.842886, -0.538019], "ImageOrientationText": "Tra>Cor(-32.6)>Sag(2.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-02_ses-004_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 625, - -7183, - -8879, - 232, - 8, - -217, - 1, - 26 - ], + "ShimSetting": [625, -7183, -8879, 232, 8, -217, 1, 26], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_epi.json b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_epi.json index 01f490600..79e261b1d 100644 --- a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999348, - 0.0113317, - 0.0342759, - 0.00889558, - 0.842886, - -0.538019 - ], + "ImageOrientationPatientDICOM": [0.999348, 0.0113317, 0.0342759, 0.00889558, 0.842886, -0.538019], "ImageOrientationText": "Tra>Cor(-32.6)>Sag(2.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-02_ses-004_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 625, - -7183, - -8879, - 232, - 8, - -217, - 1, - 26 - ], + "ShimSetting": [625, -7183, -8879, 232, 8, -217, 1, 26], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_epi.json b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_epi.json index e74f758fe..0fed02d04 100644 --- a/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-02/ses-004/fmap/sub-02_ses-004_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999348, - 0.0113317, - 0.0342759, - 0.00889558, - 0.842886, - -0.538019 - ], + "ImageOrientationPatientDICOM": [0.999348, 0.0113317, 0.0342759, 0.00889558, 0.842886, -0.538019], "ImageOrientationText": "Tra>Cor(-32.6)>Sag(2.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-02_ses-004_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 625, - -7183, - -8879, - 232, - 8, - -217, - 1, - 26 - ], + "ShimSetting": [625, -7183, -8879, 232, 8, -217, 1, 26], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 74ca442613c02a7789c6b8484444844cfa1023e4 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:33:53 -0400 Subject: [PATCH 098/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..8de003032 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = cdf05719-544a-4cc0-a0ba-20f9fe956da6 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..f45add5ab --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit f45add5abada864982269105c5c72daad8a0cffb From a83366fc3ffcde9cb6dafbd6aff9fc4b3c2f7d99 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:34:04 -0400 Subject: [PATCH 099/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..77a0dd970 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 8e0851e3-252a-488b-abdd-3db560ed7b4d diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..fecbe2dd7 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit fecbe2dd7c7d1d10db2a9f1a8717fb47e015f042 From 11a51d032cdf3377a95be7e7523cf3e0cdcb2673 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:35:22 -0400 Subject: [PATCH 100/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..51932b636 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 70f760da-429c-4118-8ec7-ba60d07a28f9 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..7e14b0e3a --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 7e14b0e3a2459bb02765e9de4c7db3f401b1fb7c From 8ad6e21285a406ce07171cea21ca87f50d499600 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:35:27 -0400 Subject: [PATCH 101/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-009_acq-axial_localizer.json | 81 +++ .../sub-02_ses-009_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-009_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-009_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-009_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-009_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-009/anat/sub-02_ses-009_scout.json | 542 ++++++++++++++++++ .../ses-009/anat/sub-02_ses-009_scout.nii.gz | 1 + ...9_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-009_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...09_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...009_task-mario3_run-01_part-mag_events.tsv | 1 + ...009_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...09_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-01_part-phase_events.tsv | 1 + ...9_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-009_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...09_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...009_task-mario3_run-02_part-mag_events.tsv | 1 + ...009_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...09_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-02_part-phase_events.tsv | 1 + ...9_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-009_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...09_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...009_task-mario3_run-03_part-mag_events.tsv | 1 + ...009_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...09_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-03_part-phase_events.tsv | 1 + ...9_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-02/ses-009/sub-02_ses-009_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-009/anat/sub-02_ses-009_acq-axial_localizer.json create mode 120000 sub-02/ses-009/anat/sub-02_ses-009_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-009/anat/sub-02_ses-009_acq-coronal_localizer.json create mode 120000 sub-02/ses-009/anat/sub-02_ses-009_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-009/anat/sub-02_ses-009_acq-sagittal_localizer.json create mode 120000 sub-02/ses-009/anat/sub-02_ses-009_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-009/anat/sub-02_ses-009_scout.json create mode 120000 sub-02/ses-009/anat/sub-02_ses-009_scout.nii.gz create mode 100644 sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 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100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..83ada7a9d --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 51 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-009/anat/sub-02_ses-009_acq-axial_localizer.json b/sub-02/ses-009/anat/sub-02_ses-009_acq-axial_localizer.json new file mode 100644 index 000000000..14d31d61f --- /dev/null +++ b/sub-02/ses-009/anat/sub-02_ses-009_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:19:40.060000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + 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new file mode 100644 index 000000000..33b1ef06d --- /dev/null +++ b/sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json @@ -0,0 +1,177 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:20:43.580000", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTime1": 0.037, + "EchoTime2": 0.001, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.998908, 0.0120328, 0.0451521, 0.0134252, 0.851635, -0.523964], + 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"WindowCenter": [4816.0, 4844.0, 4814.0], + "WindowWidth": [18662.0, 18694.0, 18666.0] + }, + "slices": {} + } +} \ No newline at end of file diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz new file mode 120000 index 000000000..8595b2413 --- /dev/null +++ b/sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/mM/Mf/MD5E-s3333571--6a6d40fc6ae1f1849b25bcb53de98f61.nii.gz/MD5E-s3333571--6a6d40fc6ae1f1849b25bcb53de98f61.nii.gz \ No newline at end of file diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json new file mode 100644 index 000000000..22aec148d --- /dev/null +++ b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json @@ -0,0 +1,149 @@ +{ + 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+} \ No newline at end of file diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz new file mode 120000 index 000000000..c5e8f6176 --- /dev/null +++ b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/w8/FW/MD5E-s1147980--b97278e9e43a2e5344ce8b6f41dfc8e4.nii.gz/MD5E-s1147980--b97278e9e43a2e5344ce8b6f41dfc8e4.nii.gz \ No newline at end of file diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json new file mode 100644 index 000000000..ee4a825aa --- /dev/null +++ b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json @@ -0,0 +1,152 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:20:33.150000", + 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a/sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-03_part-phase_sbref.nii.gz b/sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-03_part-phase_sbref.nii.gz new file mode 120000 index 000000000..ada9e715d --- /dev/null +++ b/sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-03_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/6m/Vq/MD5E-s1103299--371fdf05e714a89a825bf1fff92b4d78.nii.gz/MD5E-s1103299--371fdf05e714a89a825bf1fff92b4d78.nii.gz \ No newline at end of file diff --git a/sub-02/ses-009/sub-02_ses-009_scans.tsv b/sub-02/ses-009/sub-02_ses-009_scans.tsv new file mode 120000 index 000000000..4b0a45b9e --- /dev/null +++ b/sub-02/ses-009/sub-02_ses-009_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/pf/P9/MD5E-s2667--a0b79a716290c77eccab64f3dce00f91.tsv/MD5E-s2667--a0b79a716290c77eccab64f3dce00f91.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..3b78f77c5 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.998908, 0.0120328, 0.0451521, 0.0134252, 0.851635, -0.523964], + "ImageOrientationText": "Tra>Cor(-31.6)>Sag(2.6)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": 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"SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 307.387, + "dcmmeta_affine": [ + [-1.9978152513504028, 0.02685035951435566, 0.08951578289270401, 103.31771850585938], + [-0.024065645411610603, 1.7032694816589355, -1.0479952096939087, -47.87774658203125], + [0.09030427038669586, 1.0479276180267334, 1.7010858058929443, -106.49052429199219], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 6cc4f6032b068f8dd7508ff9b174d315537a6332 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:35:46 -0400 Subject: [PATCH 102/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-023_acq-axial_localizer.json | 81 +++ .../sub-01_ses-023_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-023_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-023_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-023_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-023_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-023/anat/sub-01_ses-023_scout.json | 542 ++++++++++++++++++ .../ses-023/anat/sub-01_ses-023_scout.nii.gz | 1 + ...3_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-023_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...23_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...023_task-mario3_run-01_part-mag_events.tsv | 1 + ...023_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...23_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-01_part-phase_events.tsv | 1 + ...3_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-023_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...23_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...023_task-mario3_run-02_part-mag_events.tsv | 1 + ...023_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...23_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-02_part-phase_events.tsv | 1 + ...3_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-023_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...23_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...023_task-mario3_run-03_part-mag_events.tsv | 1 + ...023_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...23_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-03_part-phase_events.tsv | 1 + ...3_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-01/ses-023/sub-01_ses-023_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-023/anat/sub-01_ses-023_acq-axial_localizer.json create mode 120000 sub-01/ses-023/anat/sub-01_ses-023_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-023/anat/sub-01_ses-023_acq-coronal_localizer.json create mode 120000 sub-01/ses-023/anat/sub-01_ses-023_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-023/anat/sub-01_ses-023_acq-sagittal_localizer.json create mode 120000 sub-01/ses-023/anat/sub-01_ses-023_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-023/anat/sub-01_ses-023_scout.json create mode 120000 sub-01/ses-023/anat/sub-01_ses-023_scout.nii.gz create mode 100644 sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-01/ses-023/sub-01_ses-023_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 7e14b0e3a..77cda4ee1 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 7e14b0e3a2459bb02765e9de4c7db3f401b1fb7c +Subproject commit 77cda4ee1dd8e0f181aafed4b3564386079b5a78 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..4708c7800 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 46 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-023/anat/sub-01_ses-023_acq-axial_localizer.json b/sub-01/ses-023/anat/sub-01_ses-023_acq-axial_localizer.json new file mode 100644 index 000000000..d2f15ce2e --- /dev/null +++ b/sub-01/ses-023/anat/sub-01_ses-023_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:26:14.125000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + 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+../../../.git/annex/objects/9q/V0/MD5E-s179258--77b42afa79d65e21775a46d3857fb9c3.nii.gz/MD5E-s179258--77b42afa79d65e21775a46d3857fb9c3.nii.gz \ No newline at end of file diff --git a/sub-01/ses-023/anat/sub-01_ses-023_acq-coronal_localizer.json b/sub-01/ses-023/anat/sub-01_ses-023_acq-coronal_localizer.json new file mode 100644 index 000000000..83932da01 --- /dev/null +++ b/sub-01/ses-023/anat/sub-01_ses-023_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:26:21.115000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, 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a/sub-01/ses-023/anat/sub-01_ses-023_acq-sagittal_localizer.json b/sub-01/ses-023/anat/sub-01_ses-023_acq-sagittal_localizer.json new file mode 100644 index 000000000..475a8e747 --- /dev/null +++ b/sub-01/ses-023/anat/sub-01_ses-023_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:26:7.135000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 0, + 1, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Sag", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + 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+++ b/sub-01/ses-023/anat/sub-01_ses-023_scout.json @@ -0,0 +1,542 @@ +{ + "AcquisitionMatrixPE": 160, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:25:50.992500", + "BaseResolution": 160, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 5.8e-06, + "EchoTime": 0.00137, + "FlipAngle": 8, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [0, 1, 0, 0, 0, -1], + "ImageOrientationText": "Sag", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "ND", + "NORM" +], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "3D", + "MagneticFieldStrength": 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0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 4dc3d5c0b81f00791fc2b76925a9c554b7c9c8ea Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:35:50 -0400 Subject: [PATCH 103/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-006_acq-axial_localizer.json | 81 +++ .../sub-01_ses-006_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-006_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-006_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-006_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-006_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-006/anat/sub-01_ses-006_scout.json | 671 ++++++++++++++++++ .../ses-006/anat/sub-01_ses-006_scout.nii.gz | 1 + ...6_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 +++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 +++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 ++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 ++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 ++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 ++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 ++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 ++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 ++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 ++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-006_task-mario3_run-01_part-mag_bold.json | 172 +++++ ...06_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...006_task-mario3_run-01_part-mag_events.tsv | 1 + ...006_task-mario3_run-01_part-mag_sbref.json | 150 ++++ ...6_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-01_part-phase_bold.json | 178 +++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-01_part-phase_events.tsv | 1 + ...6_task-mario3_run-01_part-phase_sbref.json | 153 ++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-006_task-mario3_run-02_part-mag_bold.json | 172 +++++ ...06_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...006_task-mario3_run-02_part-mag_events.tsv | 1 + ...006_task-mario3_run-02_part-mag_sbref.json | 150 ++++ ...6_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-02_part-phase_bold.json | 178 +++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-02_part-phase_events.tsv | 1 + ...6_task-mario3_run-02_part-phase_sbref.json | 153 ++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-006_task-mario3_run-03_part-mag_bold.json | 172 +++++ ...06_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...006_task-mario3_run-03_part-mag_events.tsv | 1 + ...006_task-mario3_run-03_part-mag_sbref.json | 150 ++++ ...6_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-03_part-phase_bold.json | 178 +++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-03_part-phase_events.tsv | 1 + ...6_task-mario3_run-03_part-phase_sbref.json | 153 ++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-01/ses-006/sub-01_ses-006_scans.tsv | 1 + task-mario3_bold.json | 75 ++ 65 files changed, 4576 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-006/anat/sub-01_ses-006_acq-axial_localizer.json create mode 120000 sub-01/ses-006/anat/sub-01_ses-006_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-006/anat/sub-01_ses-006_acq-coronal_localizer.json create mode 120000 sub-01/ses-006/anat/sub-01_ses-006_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-006/anat/sub-01_ses-006_acq-sagittal_localizer.json create mode 120000 sub-01/ses-006/anat/sub-01_ses-006_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-006/anat/sub-01_ses-006_scout.json create mode 120000 sub-01/ses-006/anat/sub-01_ses-006_scout.nii.gz create mode 100644 sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 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-0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-006/anat/sub-01_ses-006_acq-axial_localizer.json b/sub-01/ses-006/anat/sub-01_ses-006_acq-axial_localizer.json new file mode 100644 index 000000000..3f13a2dff --- /dev/null +++ b/sub-01/ses-006/anat/sub-01_ses-006_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + 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+../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-03_part-phase_sbref.json b/sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-03_part-phase_sbref.json new file mode 100644 index 000000000..aa3c87cd8 --- /dev/null +++ b/sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-03_part-phase_sbref.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "19:04:2.105000", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + 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"PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "func_task-mario3_run-03", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0668599, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "SeriesDescription": "func_task-mario3_run-03_SBRef", + "SeriesNumber": 15, + "ShimSetting": [ + 636, + -7186, + -8759, + 675, + 79, + 29, + -17, + 2 + ], + "SliceThickness": 2, + "SliceTiming": [ + 0, + 0.0975, + 0.195, + 0.2925, + 0.3925, + 0.49, + 0.5875, + 0.685, + 0.7825, + 0.8825, + 0.98, + 1.0775, + 1.175, + 1.2725, + 1.3725, + 1.47, + 1.5675, + 1.665, + 1.7625, + 1.8625, + 1.96, + 2.0575, + 2.155, + 2.2525, + 2.3525, + 2.45, + 2.5475, + 2.645, + 2.7425, + 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"N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.992363, 0.117313, 0.0381114, -0.097477, 0.935182, -0.34049], + "ImageOrientationText": "Tra>Cor(-19.6)>Sag(4.3)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0668599, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [636, -7186, -8759, 675, 79, 29, -17, 2], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 298.577, + "dcmmeta_affine": [ + [-1.9847267866134644, -0.19495393335819244, 0.1511700600385666, 111.69878387451172], + [-0.23462629318237305, 1.870363712310791, -0.6683487296104431, -55.47169494628906], + [0.07622288912534714, 0.6809790730476379, 1.8789511919021606, -50.9786376953125], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 9b38dd7b24bbcf134dffde35c0dc66952e7d7d87 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:35:58 -0400 Subject: [PATCH 104/463] fix fmap phase --- ...2_ses-009_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-009_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-009_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-009_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-009_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-009_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-02/ses-009/sub-02_ses-009_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-02/ses-009/fmap/{sub-02_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-009_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-009/fmap/{sub-02_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-009_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-009/fmap/{sub-02_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-009_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-009/fmap/{sub-02_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-009_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-009/fmap/{sub-02_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-009_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-009/fmap/{sub-02_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-009_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-009/fmap/{sub-02_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-009_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-009/fmap/{sub-02_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-009_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-009/fmap/{sub-02_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-009_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-009/fmap/{sub-02_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-009_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 33b1ef06d..000000000 --- a/sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:20:43.580000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - 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16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99890765131408, 0.01203282262246, 0.04515213534191, 0.01342517935577, 0.85163472823928, -0.5239637909399], - "ImagePositionPatient": [-843.06160803324, -756.30898547737, 350.02089844016], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.258966, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "161851.294000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.05966595491898, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "162130.141000", - "SliceLocation": -60.862655016631, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999873074, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "161851.226000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["162043.580000", "162045.070000", "162046.560000"], - "ContentTime": ["162130.143000", "162130.146000", "162130.148000"], - "InstanceCreationTime": ["162130.143000", "162130.146000", "162130.148000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4816.0, 4844.0, 4814.0], - "WindowWidth": [18662.0, 18694.0, 18666.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 8595b2413..000000000 --- a/sub-02/ses-009/fmap/sub-02_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/mM/Mf/MD5E-s3333571--6a6d40fc6ae1f1849b25bcb53de98f61.nii.gz/MD5E-s3333571--6a6d40fc6ae1f1849b25bcb53de98f61.nii.gz \ No newline at end of file diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index ee4a825aa..000000000 --- a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:20:33.150000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998908, - 0.0120328, - 0.0451521, - 0.0134252, - 0.851635, - -0.523964 - ], - "ImageOrientationText": "Tra>Cor(-31.6)>Sag(2.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.059666, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 625, - -7179, - -8882, - 244, - 24, - -256, - -10, - 23 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 307.387, - "WipMemBlock": "95501f28-e346-441f-9098-97ea85bddb03||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index ff1fdba14..000000000 --- a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/7K/mM/MD5E-s1112159--8fa992f6e42b8ca9f44ea9652696bebc.nii.gz/MD5E-s1112159--8fa992f6e42b8ca9f44ea9652696bebc.nii.gz \ No newline at end of file diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 927b21c53..000000000 --- a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:21:58.050000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998908, - 0.0120328, - 0.0451521, - 0.0134252, - 0.851635, - -0.523964 - ], - "ImageOrientationText": "Tra>Cor(-31.6)>Sag(2.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0748159, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 625, - -7179, - -8882, - 244, - 24, - -256, - -10, - 23 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 307.387, - "WipMemBlock": "4d39bbbc-c337-4699-b5c5-ba0899657433||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 9b4baf24e..000000000 --- a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/jJ/5P/MD5E-s1103238--88d3378738beabe6d8e2ec804c02bbcd.nii.gz/MD5E-s1103238--88d3378738beabe6d8e2ec804c02bbcd.nii.gz \ No newline at end of file diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 6ba1ed523..000000000 --- a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:35:38.587500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998908, - 0.0120328, - 0.0451521, - 0.0134252, - 0.851635, - -0.523964 - ], - "ImageOrientationText": "Tra>Cor(-31.6)>Sag(2.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0748159, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 625, - -7179, - -8882, - 244, - 24, - -256, - -10, - 23 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 307.387, - "WipMemBlock": "d35fa11c-325a-4867-b5e7-9ded59e45e66||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 24310420c..000000000 --- a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/F6/mK/MD5E-s1103339--b55706bb26424bfbc489a5d03435100a.nii.gz/MD5E-s1103339--b55706bb26424bfbc489a5d03435100a.nii.gz \ No newline at end of file diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 47fae16fb..000000000 --- a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:44:42.875000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998908, - 0.0120328, - 0.0451521, - 0.0134252, - 0.851635, - -0.523964 - ], - "ImageOrientationText": "Tra>Cor(-31.6)>Sag(2.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0748159, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 625, - -7179, - -8882, - 244, - 24, - -256, - -10, - 23 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 307.387, - "WipMemBlock": "18cc9765-82d8-4fee-b8d2-19ef738353c7||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index ada9e715d..000000000 --- a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/6m/Vq/MD5E-s1103299--371fdf05e714a89a825bf1fff92b4d78.nii.gz/MD5E-s1103299--371fdf05e714a89a825bf1fff92b4d78.nii.gz \ No newline at end of file diff --git a/sub-02/ses-009/sub-02_ses-009_scans.tsv b/sub-02/ses-009/sub-02_ses-009_scans.tsv index 4b0a45b9e..527f76cf6 120000 --- a/sub-02/ses-009/sub-02_ses-009_scans.tsv +++ b/sub-02/ses-009/sub-02_ses-009_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/pf/P9/MD5E-s2667--a0b79a716290c77eccab64f3dce00f91.tsv/MD5E-s2667--a0b79a716290c77eccab64f3dce00f91.tsv \ No newline at end of file +../../.git/annex/objects/9W/0m/MD5E-s2066--956bdc90bf2c961a6d21b05e832767b6.tsv/MD5E-s2066--956bdc90bf2c961a6d21b05e832767b6.tsv \ No newline at end of file From ec0f3b662a62cffab5338dda76362cf19d54624a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:36:04 -0400 Subject: [PATCH 105/463] fix complex event files --- ...g_events.tsv => sub-02_ses-009_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-02_ses-009_task-mario3_run-02_events.tsv} | 0 .../func/sub-02_ses-009_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-02_ses-009_task-mario3_run-03_events.tsv} | 0 .../func/sub-02_ses-009_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-02_ses-009_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-02/ses-009/func/{sub-02_ses-009_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-009_task-mario3_run-01_events.tsv} (100%) rename sub-02/ses-009/func/{sub-02_ses-009_task-mario3_run-01_part-phase_events.tsv => sub-02_ses-009_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-02_part-phase_events.tsv rename sub-02/ses-009/func/{sub-02_ses-009_task-mario3_run-02_part-mag_events.tsv => sub-02_ses-009_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-02_events.tsv similarity index 100% rename from sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-01_part-phase_events.tsv rename to sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-02_events.tsv diff --git a/sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-02_part-phase_events.tsv b/sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-02_part-mag_events.tsv b/sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-03_events.tsv similarity index 100% rename from sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-02_part-mag_events.tsv rename to sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-03_events.tsv diff --git a/sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-03_part-mag_events.tsv b/sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-009/func/sub-02_ses-009_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From dfb96b3f24c9cf8bc2cfbda8d296485b8761cb1e Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:36:16 -0400 Subject: [PATCH 106/463] fix fmap phase --- ...1_ses-023_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-023_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-023_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-023_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-023_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-023_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-023_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-023_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-023_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-023_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-01/ses-023/sub-01_ses-023_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-01/ses-023/fmap/{sub-01_ses-023_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-023_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-023/fmap/{sub-01_ses-023_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-023_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-023/fmap/{sub-01_ses-023_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-023_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-023/fmap/{sub-01_ses-023_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-023_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-023/fmap/{sub-01_ses-023_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-023_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-023/fmap/{sub-01_ses-023_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-023_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-023/fmap/{sub-01_ses-023_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-023_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-023/fmap/{sub-01_ses-023_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-023_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-01/ses-023/fmap/{sub-01_ses-023_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-01_ses-023_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-01/ses-023/fmap/{sub-01_ses-023_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-01_ses-023_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 61a50d0b9..000000000 --- a/sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:27:24.060000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.996003, 0.0887869, 0.00974527, -0.0785621, 0.922723, -0.377373], - "ImageOrientationText": "Tra>Cor(-22.1)>Sag(2.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - 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"StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 277.055, - "WipMemBlock": "f08db7e4-c961-42e0-ba9e-39819bf72d84||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9920059442520142, -0.15712414681911469, 0.08499594777822495, 112.65969848632812], - [-0.17757372558116913, 1.8454456329345703, -0.7501986026763916, -55.75303268432617], - [0.019490543752908707, 0.7547466158866882, 1.8520199060440063, -65.4618911743164], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.9960029732889, 0.08878686202821, 0.00974527223054, -0.0785620723373, 0.92272281420057, -0.3773733018429], - "ImagePositionPatient": [-764.37288780209, -870.70691190469, 279.91021608734], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.259086, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "112521.934000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.04762996441476, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "112811.078000", - "SliceLocation": -34.917627172282, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999647214, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "112521.855000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["112724.060000", "112725.550000", "112727.040000"], - "ContentTime": ["112811.080000", "112811.083000", "112811.085000"], - "InstanceCreationTime": ["112811.080000", "112811.083000", "112811.085000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4822.0, 4822.0, 4826.0], - "WindowWidth": [18574.0, 18576.0, 18578.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index d0ea1ea0b..000000000 --- a/sub-01/ses-023/fmap/sub-01_ses-023_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/QG/WV/MD5E-s3335451--e7fd9e20cb9e3764fd4980ebc3d57326.nii.gz/MD5E-s3335451--e7fd9e20cb9e3764fd4980ebc3d57326.nii.gz \ No newline at end of file diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 9a655b1ca..000000000 --- a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:27:13.630000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996003, - 0.0887869, - 0.00974527, - -0.0785621, - 0.922723, - -0.377373 - ], - "ImageOrientationText": "Tra>Cor(-22.1)>Sag(2.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.04763, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 595, - -7219, - -8812, - 629, - 99, - -15, - -118, - 60 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 277.055, - "WipMemBlock": "f08db7e4-c961-42e0-ba9e-39819bf72d84||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index d4f6dc626..000000000 --- a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Qm/P8/MD5E-s1112460--7f7035b931b831a31a2dd59bbe9d116f.nii.gz/MD5E-s1112460--7f7035b931b831a31a2dd59bbe9d116f.nii.gz \ No newline at end of file diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 58fdf8e6d..000000000 --- a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:28:12.922500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996003, - 0.0887869, - 0.00974527, - -0.0785621, - 0.922723, - -0.377373 - ], - "ImageOrientationText": "Tra>Cor(-22.1)>Sag(2.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0597238, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 595, - -7219, - -8812, - 629, - 99, - -15, - -118, - 60 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 277.055, - "WipMemBlock": "37ce0492-6099-4c3d-a161-92c4d83f61bf||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index df71a5fd4..000000000 --- a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/kw/f3/MD5E-s1103936--0ebf9cf046051d9acc0808dc79be0fb1.nii.gz/MD5E-s1103936--0ebf9cf046051d9acc0808dc79be0fb1.nii.gz \ No newline at end of file diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 29428c059..000000000 --- a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:38:20.412500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996003, - 0.0887869, - 0.00974527, - -0.0785621, - 0.922723, - -0.377373 - ], - "ImageOrientationText": "Tra>Cor(-22.1)>Sag(2.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0597238, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 595, - -7219, - -8812, - 629, - 99, - -15, - -118, - 60 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 277.055, - "WipMemBlock": "2646fbef-5850-457a-81fe-c9975a37c41e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index b7ac59cd7..000000000 --- a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/2p/Mg/MD5E-s1103838--f9779095ea7356335fc69d2db4d88426.nii.gz/MD5E-s1103838--f9779095ea7356335fc69d2db4d88426.nii.gz \ No newline at end of file diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 0ecba461d..000000000 --- a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:49:32.142500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996003, - 0.0887869, - 0.00974527, - -0.0785621, - 0.922723, - -0.377373 - ], - "ImageOrientationText": "Tra>Cor(-22.1)>Sag(2.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0597238, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 595, - -7219, - -8812, - 629, - 99, - -15, - -118, - 60 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 277.055, - "WipMemBlock": "90cb2438-5bff-4055-b580-ab7b4b3cfdae||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 6fee14997..000000000 --- a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Q6/xX/MD5E-s1103820--93752cd579911a2851cb7077dbbb5813.nii.gz/MD5E-s1103820--93752cd579911a2851cb7077dbbb5813.nii.gz \ No newline at end of file diff --git a/sub-01/ses-023/sub-01_ses-023_scans.tsv b/sub-01/ses-023/sub-01_ses-023_scans.tsv index 982cca863..07e1dfcca 120000 --- a/sub-01/ses-023/sub-01_ses-023_scans.tsv +++ b/sub-01/ses-023/sub-01_ses-023_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/fz/zg/MD5E-s2667--049f3c3212248826f3c2a3b1062011ac.tsv/MD5E-s2667--049f3c3212248826f3c2a3b1062011ac.tsv \ No newline at end of file +../../.git/annex/objects/Q9/zP/MD5E-s2066--d1a724ee92f06aa0bfefa6174f03a9c9.tsv/MD5E-s2066--d1a724ee92f06aa0bfefa6174f03a9c9.tsv \ No newline at end of file From ab014f6649218546956d005ec2e9e2e92d8a935f Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:36:19 -0400 Subject: [PATCH 107/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-018_acq-axial_localizer.json | 81 +++ .../sub-01_ses-018_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-018_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-018_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-018_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-018_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-018/anat/sub-01_ses-018_scout.json | 542 ++++++++++++++++++ .../ses-018/anat/sub-01_ses-018_scout.nii.gz | 1 + ...8_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-018_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...18_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...018_task-mario3_run-01_part-mag_events.tsv | 1 + ...018_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...18_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-01_part-phase_events.tsv | 1 + ...8_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-018_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...18_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...018_task-mario3_run-02_part-mag_events.tsv | 1 + ...018_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...18_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-02_part-phase_events.tsv | 1 + ...8_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-018_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...18_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...018_task-mario3_run-03_part-mag_events.tsv | 1 + ...018_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...18_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-03_part-phase_events.tsv | 1 + ...8_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-01/ses-018/sub-01_ses-018_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-018/anat/sub-01_ses-018_acq-axial_localizer.json create mode 120000 sub-01/ses-018/anat/sub-01_ses-018_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-018/anat/sub-01_ses-018_acq-coronal_localizer.json create mode 120000 sub-01/ses-018/anat/sub-01_ses-018_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-018/anat/sub-01_ses-018_acq-sagittal_localizer.json create mode 120000 sub-01/ses-018/anat/sub-01_ses-018_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-018/anat/sub-01_ses-018_scout.json create mode 120000 sub-01/ses-018/anat/sub-01_ses-018_scout.nii.gz create mode 100644 sub-01/ses-018/fmap/sub-01_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-018/fmap/sub-01_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-018/fmap/sub-01_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-018/fmap/sub-01_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-01/ses-018/sub-01_ses-018_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 7532dce19..8470c60cc 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 7532dce194be3ca1b010a1e011ee2c02884488e3 +Subproject commit 8470c60cc4e85d0292b0d7c3060b63704d9352ed diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-018/anat/sub-01_ses-018_acq-axial_localizer.json b/sub-01/ses-018/anat/sub-01_ses-018_acq-axial_localizer.json new file mode 100644 index 000000000..14d8103af --- /dev/null +++ b/sub-01/ses-018/anat/sub-01_ses-018_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "17:15:26.037500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + 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"SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 254.896 +} \ No newline at end of file diff --git a/sub-01/ses-018/anat/sub-01_ses-018_acq-axial_localizer.nii.gz b/sub-01/ses-018/anat/sub-01_ses-018_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..0598c34c5 --- /dev/null +++ b/sub-01/ses-018/anat/sub-01_ses-018_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/3G/J5/MD5E-s180625--209237847b5502b50b95d1ad316dd11d.nii.gz/MD5E-s180625--209237847b5502b50b95d1ad316dd11d.nii.gz \ No newline at end of file diff --git a/sub-01/ses-018/anat/sub-01_ses-018_acq-coronal_localizer.json b/sub-01/ses-018/anat/sub-01_ses-018_acq-coronal_localizer.json new file mode 100644 index 000000000..b3fc801c3 --- /dev/null +++ b/sub-01/ses-018/anat/sub-01_ses-018_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "17:15:33.027500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0356643, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 254.896 +} \ No newline at end of file diff --git a/sub-01/ses-018/anat/sub-01_ses-018_acq-coronal_localizer.nii.gz b/sub-01/ses-018/anat/sub-01_ses-018_acq-coronal_localizer.nii.gz new file mode 120000 index 000000000..9f5ea4f5a --- /dev/null +++ b/sub-01/ses-018/anat/sub-01_ses-018_acq-coronal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/WZ/FW/MD5E-s193006--19998cb855572f5641073d37e0c3e60c.nii.gz/MD5E-s193006--19998cb855572f5641073d37e0c3e60c.nii.gz \ No newline at end of file diff --git a/sub-01/ses-018/anat/sub-01_ses-018_acq-sagittal_localizer.json b/sub-01/ses-018/anat/sub-01_ses-018_acq-sagittal_localizer.json new file mode 100644 index 000000000..0f94fe628 --- /dev/null +++ b/sub-01/ses-018/anat/sub-01_ses-018_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "17:15:19.047500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": 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111.3165512084961], + [-0.2196793109178543, 1.8243764638900757, -0.7895515561103821, -45.51988983154297], + [0.030768873170018196, 0.7973833084106445, 1.8339120149612427, -67.08881378173828], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From cbbbf8b86c2203416c24e4d561ed6d483788b89f Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:36:21 -0400 Subject: [PATCH 108/463] fix fmap phase --- ...1_ses-006_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-006_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-006_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-01/ses-006/sub-01_ses-006_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-01/ses-006/fmap/{sub-01_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-006_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-006/fmap/{sub-01_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-006_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-006/fmap/{sub-01_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-006_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-006/fmap/{sub-01_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-006_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-006/fmap/{sub-01_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-006_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-006/fmap/{sub-01_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-006_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-006/fmap/{sub-01_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-006_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-006/fmap/{sub-01_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-006_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-01/ses-006/fmap/{sub-01_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-01_ses-006_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-01/ses-006/fmap/{sub-01_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-01_ses-006_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 19e62ba4f..000000000 --- a/sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:42:48.830000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - 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"PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.05332101204923, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "184335.557000", - "SliceLocation": -20.913212544357, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000236086, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "184044.333000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["184248.830000", "184250.320000", "184251.810000"], - "ContentTime": ["184335.559000", "184335.561000", "184335.564000"], - "InstanceCreationTime": ["184335.559000", "184335.561000", "184335.564000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4794.0, 4796.0, 4792.0], - "WindowWidth": [18558.0, 18560.0, 18560.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 75d59b64c..000000000 --- a/sub-01/ses-006/fmap/sub-01_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/V6/G8/MD5E-s3335526--e39b55b8b1681875a65ae6834bc920e4.nii.gz/MD5E-s3335526--e39b55b8b1681875a65ae6834bc920e4.nii.gz \ No newline at end of file diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 7151f9d8e..000000000 --- a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:42:38.400000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992363, - 0.117313, - 0.0381114, - -0.097477, - 0.935182, - -0.34049 - ], - "ImageOrientationText": "Tra>Cor(-19.6)>Sag(4.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.053321, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 636, - -7186, - -8759, - 675, - 79, - 29, - -17, - 2 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 298.577, - "WipMemBlock": "65f3676a-799d-477b-b961-21ec8975cd4e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index ff053a298..000000000 --- a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/88/WP/MD5E-s1112379--c8915fcb562121bf91bc63bf91ccad68.nii.gz/MD5E-s1112379--c8915fcb562121bf91bc63bf91ccad68.nii.gz \ No newline at end of file diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 63c432091..000000000 --- a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:43:52.085000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992363, - 0.117313, - 0.0381114, - -0.097477, - 0.935182, - -0.34049 - ], - "ImageOrientationText": "Tra>Cor(-19.6)>Sag(4.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0668599, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 636, - -7186, - -8759, - 675, - 79, - 29, - -17, - 2 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 298.577, - "WipMemBlock": "4dcdc2d7-a141-48e5-95e2-6dfe8d3e1e84||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index f2a910533..000000000 --- a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/KJ/Jk/MD5E-s1103755--cd538be2d011e36124d55684cc274d60.nii.gz/MD5E-s1103755--cd538be2d011e36124d55684cc274d60.nii.gz \ No newline at end of file diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index f3f61f189..000000000 --- a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:53:59.860000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992363, - 0.117313, - 0.0381114, - -0.097477, - 0.935182, - -0.34049 - ], - "ImageOrientationText": "Tra>Cor(-19.6)>Sag(4.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0668599, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 636, - -7186, - -8759, - 675, - 79, - 29, - -17, - 2 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 298.577, - "WipMemBlock": "c90fdcad-07ee-4906-90cc-853bfd59d208||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 8a934a6ed..000000000 --- a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/mv/x8/MD5E-s1103666--1634f9beadb1abed8dc6a36edb5258ca.nii.gz/MD5E-s1103666--1634f9beadb1abed8dc6a36edb5258ca.nii.gz \ No newline at end of file diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 0d4423b05..000000000 --- a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:04:2.105000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992363, - 0.117313, - 0.0381114, - -0.097477, - 0.935182, - -0.34049 - ], - "ImageOrientationText": "Tra>Cor(-19.6)>Sag(4.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0668599, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 636, - -7186, - -8759, - 675, - 79, - 29, - -17, - 2 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 298.577, - "WipMemBlock": "8cbb12d6-dbb3-44cc-a859-959d598d05e3||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index d6b22f837..000000000 --- a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/m2/7p/MD5E-s1103785--e8934740e498d55e1497035e9b2af0f9.nii.gz/MD5E-s1103785--e8934740e498d55e1497035e9b2af0f9.nii.gz \ No newline at end of file diff --git a/sub-01/ses-006/sub-01_ses-006_scans.tsv b/sub-01/ses-006/sub-01_ses-006_scans.tsv index e707a895f..a46339eed 120000 --- a/sub-01/ses-006/sub-01_ses-006_scans.tsv +++ b/sub-01/ses-006/sub-01_ses-006_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/v7/PZ/MD5E-s2667--cfe4a619ec73fa1115818e8d46f31f14.tsv/MD5E-s2667--cfe4a619ec73fa1115818e8d46f31f14.tsv \ No newline at end of file +../../.git/annex/objects/m2/jV/MD5E-s2066--d42c839e12ec93d09424c5985419c5bc.tsv/MD5E-s2066--d42c839e12ec93d09424c5985419c5bc.tsv \ No newline at end of file From dab54ec55a675c89473c75fa61d6a7ac3cbdf5a0 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:36:22 -0400 Subject: [PATCH 109/463] fix complex event files --- ...g_events.tsv => sub-01_ses-023_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-023_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-023_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-01_ses-023_task-mario3_run-03_events.tsv} | 0 .../func/sub-01_ses-023_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-01_ses-023_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-01/ses-023/func/{sub-01_ses-023_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-023_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-023/func/{sub-01_ses-023_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-023_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-02_part-phase_events.tsv rename sub-01/ses-023/func/{sub-01_ses-023_task-mario3_run-02_part-mag_events.tsv => sub-01_ses-023_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_events.tsv similarity index 100% rename from sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-02_part-mag_events.tsv rename to sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_events.tsv diff --git a/sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_part-mag_events.tsv b/sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-023/func/sub-01_ses-023_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From f88f7b0f5404a04124f7bcd8a3830855234a145a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:36:27 -0400 Subject: [PATCH 110/463] fix complex event files --- ...g_events.tsv => sub-01_ses-006_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-006_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-006_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-01_ses-006_task-mario3_run-03_events.tsv} | 0 .../func/sub-01_ses-006_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-01_ses-006_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-01/ses-006/func/{sub-01_ses-006_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-006_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-006/func/{sub-01_ses-006_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-006_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-02_part-phase_events.tsv rename sub-01/ses-006/func/{sub-01_ses-006_task-mario3_run-02_part-mag_events.tsv => sub-01_ses-006_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-03_events.tsv similarity index 100% rename from sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-02_part-mag_events.tsv rename to sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-03_events.tsv diff --git a/sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-03_part-mag_events.tsv b/sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-006/func/sub-01_ses-006_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 52fe16e2747d4229cfa44566b23ba1f7c9babb12 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:36:52 -0400 Subject: [PATCH 111/463] fix fmap phase --- ...1_ses-018_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-018_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-018_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-018_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-018_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-018_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-01/ses-018/sub-01_ses-018_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-01/ses-018/fmap/{sub-01_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-018_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-018/fmap/{sub-01_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-018_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-018/fmap/sub-01_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-018/fmap/sub-01_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-018/fmap/{sub-01_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-018_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-018/fmap/{sub-01_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-018_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-018/fmap/{sub-01_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-018_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-018/fmap/{sub-01_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-018_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-018/fmap/{sub-01_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-018_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-018/fmap/{sub-01_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-018_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-01/ses-018/fmap/{sub-01_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-01_ses-018_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-01/ses-018/fmap/{sub-01_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-01_ses-018_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-01/ses-018/fmap/sub-01_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-018/fmap/sub-01_ses-018_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-018/fmap/sub-01_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-018/fmap/sub-01_ses-018_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-018/fmap/sub-01_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-018/fmap/sub-01_ses-018_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-018/fmap/sub-01_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-018/fmap/sub-01_ses-018_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-018/fmap/sub-01_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-018/fmap/sub-01_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index aaf12ffd1..000000000 --- a/sub-01/ses-018/fmap/sub-01_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "17:16:26.067500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.99383, 0.10984, 0.0153844, -0.0946447, 0.912188, -0.398692], - "ImageOrientationText": "Tra>Cor(-23.3)>Sag(3.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": 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"456f2159-1d32-44ce-b195-c103134d7d4e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.987660527229309, -0.18928945064544678, 0.11565130949020386, 111.3165512084961], - [-0.2196793109178543, 1.8243764638900757, -0.7895515561103821, -45.51988983154297], - [0.030768873170018196, 0.7973833084106445, 1.8339120149612427, -67.08881378173828], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.9938302519543, 0.10983965324194, 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sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 8694e662b..000000000 --- a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "17:16:15.637500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of 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b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 9f3dff055..000000000 --- a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Vj/vf/MD5E-s1112282--27a6ea28319decf390c662f94e112411.nii.gz/MD5E-s1112282--27a6ea28319decf390c662f94e112411.nii.gz \ No newline at end of file diff --git a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 607c6b824..000000000 --- a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "17:17:48.060000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 60afeeefc..000000000 --- a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "17:29:32.850000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99383, - 0.10984, - 0.0153844, - -0.0946447, - 0.912188, - -0.398692 - ], - "ImageOrientationText": "Tra>Cor(-23.3)>Sag(3.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.05253, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 617, - -7199, - -8827, - 602, - 81, - -27, - -77, - 8 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 254.896, - "WipMemBlock": "ac13696c-05fe-4335-a1fc-a4daa2274112||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 86bc92bfd..000000000 --- a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/x3/3f/MD5E-s1103929--7185f2981f6a226511ce759507fefb33.nii.gz/MD5E-s1103929--7185f2981f6a226511ce759507fefb33.nii.gz \ No newline at end of file diff --git a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index c07138514..000000000 --- a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "17:44:22.545000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99383, - 0.10984, - 0.0153844, - -0.0946447, - 0.912188, - -0.398692 - ], - "ImageOrientationText": "Tra>Cor(-23.3)>Sag(3.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.05253, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 617, - -7199, - -8827, - 602, - 81, - -27, - -77, - 8 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 254.896, - "WipMemBlock": "bf8b6f96-79c2-499c-941d-08df5dfa8664||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index c1e105963..000000000 --- a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/WZ/qx/MD5E-s1103851--3386f7e6221a79c3de47e548f0d58f9f.nii.gz/MD5E-s1103851--3386f7e6221a79c3de47e548f0d58f9f.nii.gz \ No newline at end of file diff --git a/sub-01/ses-018/sub-01_ses-018_scans.tsv b/sub-01/ses-018/sub-01_ses-018_scans.tsv index b86dc3a4c..c491434fa 120000 --- a/sub-01/ses-018/sub-01_ses-018_scans.tsv +++ b/sub-01/ses-018/sub-01_ses-018_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/3q/8X/MD5E-s2660--597375776c735c99ec9bb4fdf4f6e9f3.tsv/MD5E-s2660--597375776c735c99ec9bb4fdf4f6e9f3.tsv \ No newline at end of file +../../.git/annex/objects/2G/k9/MD5E-s2059--d1316ccdb70e97564156940ed0550c7e.tsv/MD5E-s2059--d1316ccdb70e97564156940ed0550c7e.tsv \ No newline at end of file From f300b6df2ae48e874a99073b32a9d6c41d29627b Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:36:59 -0400 Subject: [PATCH 112/463] fix complex event files --- ...g_events.tsv => sub-01_ses-018_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-018_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-018_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-01_ses-018_task-mario3_run-03_events.tsv} | 0 .../func/sub-01_ses-018_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-01_ses-018_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-01/ses-018/func/{sub-01_ses-018_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-018_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-018/func/{sub-01_ses-018_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-018_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-02_part-phase_events.tsv rename sub-01/ses-018/func/{sub-01_ses-018_task-mario3_run-02_part-mag_events.tsv => sub-01_ses-018_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_events.tsv similarity index 100% rename from sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-02_part-mag_events.tsv rename to sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_events.tsv diff --git a/sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_part-mag_events.tsv b/sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-018/func/sub-01_ses-018_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 4f4f71ac3873b49b341e105ac6f90f7cac7707d5 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:37:20 -0400 Subject: [PATCH 113/463] fill IntendedFor --- ...2_ses-009_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...2_ses-009_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...2_ses-009_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...2_ses-009_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_epi.json index 22aec148d..7689cac3d 100644 --- a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998908, - 0.0120328, - 0.0451521, - 0.0134252, - 0.851635, - -0.523964 - ], + "ImageOrientationPatientDICOM": [0.998908, 0.0120328, 0.0451521, 0.0134252, 0.851635, -0.523964], "ImageOrientationText": "Tra>Cor(-31.6)>Sag(2.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-009/func/sub-02_ses-009_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-009/func/sub-02_ses-009_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-009/func/sub-02_ses-009_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 625, - -7179, - -8882, - 244, - 24, - -256, - -10, - 23 - ], + "ShimSetting": [625, -7179, -8882, 244, 24, -256, -10, 23], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_epi.json b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_epi.json index e6a4fc2bb..0136f2349 100644 --- a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998908, - 0.0120328, - 0.0451521, - 0.0134252, - 0.851635, - -0.523964 - ], + "ImageOrientationPatientDICOM": [0.998908, 0.0120328, 0.0451521, 0.0134252, 0.851635, -0.523964], "ImageOrientationText": "Tra>Cor(-31.6)>Sag(2.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-009/func/sub-02_ses-009_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 625, - -7179, - -8882, - 244, - 24, - -256, - -10, - 23 - ], + "ShimSetting": [625, -7179, -8882, 244, 24, -256, -10, 23], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_epi.json b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_epi.json index ffca22ef9..b72973c60 100644 --- a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998908, - 0.0120328, - 0.0451521, - 0.0134252, - 0.851635, - -0.523964 - ], + "ImageOrientationPatientDICOM": [0.998908, 0.0120328, 0.0451521, 0.0134252, 0.851635, -0.523964], "ImageOrientationText": "Tra>Cor(-31.6)>Sag(2.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-009/func/sub-02_ses-009_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 625, - -7179, - -8882, - 244, - 24, - -256, - -10, - 23 - ], + "ShimSetting": [625, -7179, -8882, 244, 24, -256, -10, 23], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_epi.json b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_epi.json index cb96825eb..28afa6fb4 100644 --- a/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-02/ses-009/fmap/sub-02_ses-009_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998908, - 0.0120328, - 0.0451521, - 0.0134252, - 0.851635, - -0.523964 - ], + "ImageOrientationPatientDICOM": [0.998908, 0.0120328, 0.0451521, 0.0134252, 0.851635, -0.523964], "ImageOrientationText": "Tra>Cor(-31.6)>Sag(2.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-009/func/sub-02_ses-009_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 625, - -7179, - -8882, - 244, - 24, - -256, - -10, - 23 - ], + "ShimSetting": [625, -7179, -8882, 244, 24, -256, -10, 23], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.9775, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 870f8f97c02acbd9372b3460eb52ce96a517e63f Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:37:22 -0400 Subject: [PATCH 114/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..0d28b14c8 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = e4a59c61-25f7-4720-a676-dfb34c7732c0 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..33fb476f0 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 33fb476f069f0dac74b09ccfda9f3d9ceff42972 From 1ed65643e15745d926a5e36d056f05d3ef550948 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:37:31 -0400 Subject: [PATCH 115/463] fill IntendedFor --- ...1_ses-023_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...1_ses-023_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-023_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...1_ses-023_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_epi.json index 0aba02bb3..cf9da876d 100644 --- a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996003, - 0.0887869, - 0.00974527, - -0.0785621, - 0.922723, - -0.377373 - ], + "ImageOrientationPatientDICOM": [0.996003, 0.0887869, 0.00974527, -0.0785621, 0.922723, -0.377373], "ImageOrientationText": "Tra>Cor(-22.1)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-023/func/sub-01_ses-023_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-023/func/sub-01_ses-023_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-023/func/sub-01_ses-023_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 595, - -7219, - -8812, - 629, - 99, - -15, - -118, - 60 - ], + "ShimSetting": [595, -7219, -8812, 629, 99, -15, -118, 60], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_epi.json index cadd7009e..b2fb7354c 100644 --- a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996003, - 0.0887869, - 0.00974527, - -0.0785621, - 0.922723, - -0.377373 - ], + "ImageOrientationPatientDICOM": [0.996003, 0.0887869, 0.00974527, -0.0785621, 0.922723, -0.377373], "ImageOrientationText": "Tra>Cor(-22.1)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-023/func/sub-01_ses-023_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 595, - -7219, - -8812, - 629, - 99, - -15, - -118, - 60 - ], + "ShimSetting": [595, -7219, -8812, 629, 99, -15, -118, 60], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_epi.json index db78861a9..3e8b05f92 100644 --- a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996003, - 0.0887869, - 0.00974527, - -0.0785621, - 0.922723, - -0.377373 - ], + "ImageOrientationPatientDICOM": [0.996003, 0.0887869, 0.00974527, -0.0785621, 0.922723, -0.377373], "ImageOrientationText": "Tra>Cor(-22.1)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-023/func/sub-01_ses-023_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 595, - -7219, - -8812, - 629, - 99, - -15, - -118, - 60 - ], + "ShimSetting": [595, -7219, -8812, 629, 99, -15, -118, 60], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_epi.json b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_epi.json index b99fdb939..79c50d442 100644 --- a/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-01/ses-023/fmap/sub-01_ses-023_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996003, - 0.0887869, - 0.00974527, - -0.0785621, - 0.922723, - -0.377373 - ], + "ImageOrientationPatientDICOM": [0.996003, 0.0887869, 0.00974527, -0.0785621, 0.922723, -0.377373], "ImageOrientationText": "Tra>Cor(-22.1)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-023/func/sub-01_ses-023_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 595, - -7219, - -8812, - 629, - 99, - -15, - -118, - 60 - ], + "ShimSetting": [595, -7219, -8812, 629, 99, -15, -118, 60], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From ee2b3c30ca04a629b9295b2b5c5cd340f0e481e7 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:37:35 -0400 Subject: [PATCH 116/463] fill IntendedFor --- ...1_ses-006_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...1_ses-006_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-006_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...1_ses-006_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_epi.json index 1a4e3d096..9bb91f9b1 100644 --- a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992363, - 0.117313, - 0.0381114, - -0.097477, - 0.935182, - -0.34049 - ], + "ImageOrientationPatientDICOM": [0.992363, 0.117313, 0.0381114, -0.097477, 0.935182, -0.34049], "ImageOrientationText": "Tra>Cor(-19.6)>Sag(4.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-01_ses-006_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-006/func/sub-01_ses-006_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-006/func/sub-01_ses-006_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 636, - -7186, - -8759, - 675, - 79, - 29, - -17, - 2 - ], + "ShimSetting": [636, -7186, -8759, 675, 79, 29, -17, 2], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_epi.json index 4301c751c..6a246d7cc 100644 --- a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992363, - 0.117313, - 0.0381114, - -0.097477, - 0.935182, - -0.34049 - ], + "ImageOrientationPatientDICOM": [0.992363, 0.117313, 0.0381114, -0.097477, 0.935182, -0.34049], "ImageOrientationText": "Tra>Cor(-19.6)>Sag(4.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-01_ses-006_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 636, - -7186, - -8759, - 675, - 79, - 29, - -17, - 2 - ], + "ShimSetting": [636, -7186, -8759, 675, 79, 29, -17, 2], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_epi.json index cc58a19df..c6177b0e6 100644 --- a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992363, - 0.117313, - 0.0381114, - -0.097477, - 0.935182, - -0.34049 - ], + "ImageOrientationPatientDICOM": [0.992363, 0.117313, 0.0381114, -0.097477, 0.935182, -0.34049], "ImageOrientationText": "Tra>Cor(-19.6)>Sag(4.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-01_ses-006_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 636, - -7186, - -8759, - 675, - 79, - 29, - -17, - 2 - ], + "ShimSetting": [636, -7186, -8759, 675, 79, 29, -17, 2], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_epi.json b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_epi.json index bddda962f..0d8e9a870 100644 --- a/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-01/ses-006/fmap/sub-01_ses-006_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992363, - 0.117313, - 0.0381114, - -0.097477, - 0.935182, - -0.34049 - ], + "ImageOrientationPatientDICOM": [0.992363, 0.117313, 0.0381114, -0.097477, 0.935182, -0.34049], "ImageOrientationText": "Tra>Cor(-19.6)>Sag(4.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-01_ses-006_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 636, - -7186, - -8759, - 675, - 79, - 29, - -17, - 2 - ], + "ShimSetting": [636, -7186, -8759, 675, 79, 29, -17, 2], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From faa7644239f77fe067d1848d44b36d2e15a865dc Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:37:49 -0400 Subject: [PATCH 117/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-002_acq-axial_localizer.json | 81 +++ .../sub-02_ses-002_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-002_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-002_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-002_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-002_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-002/anat/sub-02_ses-002_scout.json | 542 ++++++++++++++++++ .../ses-002/anat/sub-02_ses-002_scout.nii.gz | 1 + ...2_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-002_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-01_part-mag_events.tsv | 1 + ...002_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-01_part-phase_events.tsv | 1 + ...2_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-002_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-02_part-mag_events.tsv | 1 + ...002_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-02_part-phase_events.tsv | 1 + ...2_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-002_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-03_part-mag_events.tsv | 1 + ...002_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-03_part-phase_events.tsv | 1 + ...2_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-002_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-04_part-mag_events.tsv | 1 + ...002_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-04_part-phase_events.tsv | 1 + ...2_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-02/ses-002/sub-02_ses-002_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5409 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-002/anat/sub-02_ses-002_acq-axial_localizer.json create mode 120000 sub-02/ses-002/anat/sub-02_ses-002_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-002/anat/sub-02_ses-002_acq-coronal_localizer.json create mode 120000 sub-02/ses-002/anat/sub-02_ses-002_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-002/anat/sub-02_ses-002_acq-sagittal_localizer.json create mode 120000 sub-02/ses-002/anat/sub-02_ses-002_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-002/anat/sub-02_ses-002_scout.json create mode 120000 sub-02/ses-002/anat/sub-02_ses-002_scout.nii.gz create mode 100644 sub-02/ses-002/fmap/sub-02_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-002/fmap/sub-02_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-002/fmap/sub-02_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-002/fmap/sub-02_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_sbref.nii.gz create mode 120000 sub-02/ses-002/sub-02_ses-002_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 33fb476f0..fcfa70e8f 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 33fb476f069f0dac74b09ccfda9f3d9ceff42972 +Subproject commit fcfa70e8f8d052c56572d4a219218793e9ac5c9d diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..9a376537e --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-002/anat/sub-02_ses-002_acq-axial_localizer.json b/sub-02/ses-002/anat/sub-02_ses-002_acq-axial_localizer.json new file mode 100644 index 000000000..19a352a5d --- /dev/null +++ b/sub-02/ses-002/anat/sub-02_ses-002_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:14:7.012500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + 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b/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_bold.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/zg/Z9/MD5E-s349352036--adf3e3ef886a37f67fe5b232cbbea2c0.nii.gz/MD5E-s349352036--adf3e3ef886a37f67fe5b232cbbea2c0.nii.gz \ No newline at end of file diff --git a/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_events.tsv b/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_events.tsv new file mode 120000 index 000000000..1bbdfddb5 --- /dev/null +++ b/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_events.tsv @@ -0,0 +1 @@ +../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_sbref.json b/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_sbref.json new file mode 100644 index 000000000..92914c102 --- /dev/null +++ b/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_sbref.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:44:40.562500", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTime1": 0.037, + "EchoTime2": 0.001, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Single-band reference", + "ImageOrientationPatientDICOM": [ + 0.998714, + 0.00370923, + 0.0505703, + 0.0231871, + 0.85353, + -0.520527 + ], + "ImageOrientationText": "Tra>Cor(-31.4)>Sag(2.6)", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "P", + "ND", + "MOSAIC", + "PHASE" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "func_task-mario3_run-04", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0564705, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "SeriesDescription": "func_task-mario3_run-04_SBRef", + "SeriesNumber": 18, + "ShimSetting": [ + 624, + -7178, + -8864, + 275, + 44, + -177, + -50, + 17 + ], + "SliceThickness": 2, + "SliceTiming": [ + 0, + 0.0975, + 0.195, + 0.2925, + 0.3925, + 0.49, + 0.5875, + 0.685, + 0.7825, + 0.8825, + 0.98, + 1.0775, + 1.175, + 1.2725, + 1.3725, + 1.47, + 1.5675, + 1.665, + 1.7625, + 1.8625, + 1.96, + 2.0575, + 2.155, + 2.2525, + 2.3525, + 2.45, + 2.5475, + 2.645, + 2.7425, + 2.84, + 2.94, + 3.0375, + 3.135, + 3.2325, + 3.33, + 3.43, + 3.5275, + 3.625, + 3.7225, + 3.82, + 3.92, + 4.0175, + 4.115, + 4.2125, + 4.31, + 4.41, + 4.5075, + 4.605, + 4.7025, + 4.8, + 4.9, + 4.9975, + 5.095, + 5.1925, + 5.29, + 5.39, + 5.4875, + 5.585, + 5.6825, + 5.78 + ], + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 276.172, + "WipMemBlock": "331b7e7d-8560-4d15-bc96-dac853911540||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_sbref.nii.gz b/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_sbref.nii.gz new file mode 120000 index 000000000..8fbc66fc3 --- /dev/null +++ b/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/86/W5/MD5E-s1103069--8b06e7a3994e01f08124caeae6ac39d5.nii.gz/MD5E-s1103069--8b06e7a3994e01f08124caeae6ac39d5.nii.gz \ No newline at end of file diff --git a/sub-02/ses-002/sub-02_ses-002_scans.tsv b/sub-02/ses-002/sub-02_ses-002_scans.tsv new file mode 120000 index 000000000..53ccc22b3 --- /dev/null +++ b/sub-02/ses-002/sub-02_ses-002_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/55/zm/MD5E-s3289--ab90532322bce9cb229165c1ebbba5d6.tsv/MD5E-s3289--ab90532322bce9cb229165c1ebbba5d6.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..5eae8bd9d --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.998714, 0.00370923, 0.0505703, 0.0231871, 0.85353, -0.520527], + "ImageOrientationText": "Tra>Cor(-31.4)>Sag(2.6)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0564705, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [624, -7178, -8864, 275, 44, -177, -50, 17], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 276.172, + "dcmmeta_affine": [ + [-1.997427225112915, 0.04637422785162926, 0.0901881605386734, 103.13511657714844], + [-0.007418454624712467, 1.7070608139038086, -1.0420596599578857, -49.934730529785156], + [0.10114069283008575, 1.0410537719726562, 1.7046928405761719, -102.40422821044922], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 3550d4469ab8c12a455ce4b194333ca154a61bb7 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:38:08 -0400 Subject: [PATCH 118/463] fill IntendedFor --- ...1_ses-018_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...1_ses-018_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-018_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...1_ses-018_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_epi.json index 0e09386d6..e546df9d3 100644 --- a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99383, - 0.10984, - 0.0153844, - -0.0946447, - 0.912188, - -0.398692 - ], + "ImageOrientationPatientDICOM": [0.99383, 0.10984, 0.0153844, -0.0946447, 0.912188, -0.398692], "ImageOrientationText": "Tra>Cor(-23.3)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-01_ses-018_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-018/func/sub-01_ses-018_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-018/func/sub-01_ses-018_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 617, - -7199, - -8827, - 602, - 81, - -27, - -77, - 8 - ], + "ShimSetting": [617, -7199, -8827, 602, 81, -27, -77, 8], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_epi.json index 0b0f085ba..2df0d2770 100644 --- a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99383, - 0.10984, - 0.0153844, - -0.0946447, - 0.912188, - -0.398692 - ], + "ImageOrientationPatientDICOM": [0.99383, 0.10984, 0.0153844, -0.0946447, 0.912188, -0.398692], "ImageOrientationText": "Tra>Cor(-23.3)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-01_ses-018_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 617, - -7199, - -8827, - 602, - 81, - -27, - -77, - 8 - ], + "ShimSetting": [617, -7199, -8827, 602, 81, -27, -77, 8], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-02_epi.json index 670b11ce7..7dc50ca38 100644 --- a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99383, - 0.10984, - 0.0153844, - -0.0946447, - 0.912188, - -0.398692 - ], + "ImageOrientationPatientDICOM": [0.99383, 0.10984, 0.0153844, -0.0946447, 0.912188, -0.398692], "ImageOrientationText": "Tra>Cor(-23.3)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-01_ses-018_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 617, - -7199, - -8827, - 602, - 81, - -27, - -77, - 8 - ], + "ShimSetting": [617, -7199, -8827, 602, 81, -27, -77, 8], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.4875, 0.5875, 0.685, 0.7825, 0.88, 0.9775, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.485, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_epi.json b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_epi.json index 5434406e3..2d3dcc3a5 100644 --- a/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-01/ses-018/fmap/sub-01_ses-018_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99383, - 0.10984, - 0.0153844, - -0.0946447, - 0.912188, - -0.398692 - ], + "ImageOrientationPatientDICOM": [0.99383, 0.10984, 0.0153844, -0.0946447, 0.912188, -0.398692], "ImageOrientationText": "Tra>Cor(-23.3)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-01_ses-018_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 617, - -7199, - -8827, - 602, - 81, - -27, - -77, - 8 - ], + "ShimSetting": [617, -7199, -8827, 602, 81, -27, -77, 8], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 838efe67acf893048b93c8f7622200c1ddbbae72 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:38:29 -0400 Subject: [PATCH 119/463] fix fmap phase --- ...2_ses-002_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-002_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-002_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-02/ses-002/sub-02_ses-002_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-02/ses-002/fmap/{sub-02_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-002_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-002/fmap/{sub-02_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-002_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-002/fmap/sub-02_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-002/fmap/sub-02_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-002/fmap/{sub-02_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-002_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-002/fmap/{sub-02_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-002_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-002/fmap/{sub-02_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-002_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-002/fmap/{sub-02_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-002_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-002/fmap/{sub-02_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-002_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-002/fmap/{sub-02_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-002_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-002/fmap/{sub-02_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-002_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-002/fmap/{sub-02_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-002_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-02/ses-002/fmap/{sub-02_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-02_ses-002_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-02/ses-002/fmap/{sub-02_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-02_ses-002_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-002/fmap/sub-02_ses-002_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-002/fmap/sub-02_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-002/fmap/sub-02_ses-002_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-002/fmap/sub-02_ses-002_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-002/fmap/sub-02_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-002/fmap/sub-02_ses-002_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-002/fmap/sub-02_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 4b96d923d..000000000 --- a/sub-02/ses-002/fmap/sub-02_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:15:8.455000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.998714, 0.00370923, 0.0505703, 0.0231871, 0.85353, -0.520527], - "ImageOrientationText": "Tra>Cor(-31.4)>Sag(2.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0450354, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [624, -7178, -8864, 275, 44, -177, -50, 17], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875, 0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875, 0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875, 0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 276.172, - "WipMemBlock": "8e8a6890-3668-4d71-86db-88c1302f3d46||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.997427225112915, 0.04637422785162926, 0.0901881605386734, 103.13511657714844], - [-0.007418454624712467, 1.7070608139038086, -1.0420596599578857, -49.934730529785156], - [0.10114069283008575, 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"LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "161315.250000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.04503541493078, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "161554.681000", - "SliceLocation": -56.615607256398, - "SliceThickness": 2.0, - 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index 1a75215ae..000000000 --- a/sub-02/ses-002/fmap/sub-02_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/x2/Gz/MD5E-s3333159--72d74d2aa256aa60416f8c331a80e66f.nii.gz/MD5E-s3333159--72d74d2aa256aa60416f8c331a80e66f.nii.gz \ No newline at end of file diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 66770de1d..000000000 --- a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:14:58.025000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998714, - 0.00370923, - 0.0505703, - 0.0231871, - 0.85353, - -0.520527 - ], - "ImageOrientationText": "Tra>Cor(-31.4)>Sag(2.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0450354, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 624, - -7178, - -8864, - 275, - 44, - -177, - -50, - 17 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 276.172, - "WipMemBlock": "8e8a6890-3668-4d71-86db-88c1302f3d46||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 6f89668ef..000000000 --- a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/45/GP/MD5E-s1112023--a075d2a3a7849d1406d7c647650fb1fc.nii.gz/MD5E-s1112023--a075d2a3a7849d1406d7c647650fb1fc.nii.gz \ No newline at end of file diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 709781f5a..000000000 --- a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:16:15.400000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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"%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0564705, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 624, - -7178, - -8864, - 275, - 44, - -177, - -50, - 17 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 276.172, - "WipMemBlock": "8b1a0fa4-244f-477f-b530-5188c38c80a2||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index f54bf58a9..000000000 --- a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/PZ/qQ/MD5E-s1103170--7937f12a4cb21c712ace3393e52238cd.nii.gz/MD5E-s1103170--7937f12a4cb21c712ace3393e52238cd.nii.gz \ No newline at end of file diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 23d811940..000000000 --- a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:26:58.157500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998714, - 0.00370923, - 0.0505703, - 0.0231871, - 0.85353, - -0.520527 - ], - "ImageOrientationText": "Tra>Cor(-31.4)>Sag(2.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0564705, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 624, - -7178, - -8864, - 275, - 44, - -177, - -50, - 17 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 276.172, - "WipMemBlock": "76de5c3d-4f46-4ee5-9e35-73f14c05802b||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 1ee1b8af0..000000000 --- a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/wK/77/MD5E-s1103133--577890d152a1517e3099903238efb07e.nii.gz/MD5E-s1103133--577890d152a1517e3099903238efb07e.nii.gz \ No newline at end of file diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 3c0834e61..000000000 --- a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:35:30.990000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998714, - 0.00370923, - 0.0505703, - 0.0231871, - 0.85353, - -0.520527 - ], - "ImageOrientationText": "Tra>Cor(-31.4)>Sag(2.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0564705, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 624, - -7178, - -8864, - 275, - 44, - -177, - -50, - 17 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 276.172, - "WipMemBlock": "304ab512-de31-4752-842f-41f6d65314d2||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 819ef0b69..000000000 --- a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/kq/gg/MD5E-s1103046--47171a1a83bf2e67a244f3541d54f650.nii.gz/MD5E-s1103046--47171a1a83bf2e67a244f3541d54f650.nii.gz \ No newline at end of file diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 4ddb0bf5a..000000000 --- a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:44:40.562500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998714, - 0.00370923, - 0.0505703, - 0.0231871, - 0.85353, - -0.520527 - ], - "ImageOrientationText": "Tra>Cor(-31.4)>Sag(2.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0564705, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 624, - -7178, - -8864, - 275, - 44, - -177, - -50, - 17 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 276.172, - "WipMemBlock": "331b7e7d-8560-4d15-bc96-dac853911540||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 8fbc66fc3..000000000 --- a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/86/W5/MD5E-s1103069--8b06e7a3994e01f08124caeae6ac39d5.nii.gz/MD5E-s1103069--8b06e7a3994e01f08124caeae6ac39d5.nii.gz \ No newline at end of file diff --git a/sub-02/ses-002/sub-02_ses-002_scans.tsv b/sub-02/ses-002/sub-02_ses-002_scans.tsv index 53ccc22b3..772e9b82f 120000 --- a/sub-02/ses-002/sub-02_ses-002_scans.tsv +++ b/sub-02/ses-002/sub-02_ses-002_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/55/zm/MD5E-s3289--ab90532322bce9cb229165c1ebbba5d6.tsv/MD5E-s3289--ab90532322bce9cb229165c1ebbba5d6.tsv \ No newline at end of file +../../.git/annex/objects/1j/q2/MD5E-s2567--fdabcc70c4f64d536523e9a132164447.tsv/MD5E-s2567--fdabcc70c4f64d536523e9a132164447.tsv \ No newline at end of file From 75e22c77cc50d4a78e2f96f9e86da9086adc5a7d Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:38:38 -0400 Subject: [PATCH 120/463] fix complex event files --- ...g_events.tsv => sub-02_ses-002_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-02_ses-002_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-02_ses-002_task-mario3_run-03_events.tsv} | 0 .../func/sub-02_ses-002_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-02_ses-002_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-02_ses-002_task-mario3_run-04_events.tsv} | 0 .../func/sub-02_ses-002_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-02_ses-002_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-02/ses-002/func/{sub-02_ses-002_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-002_task-mario3_run-01_events.tsv} (100%) rename sub-02/ses-002/func/{sub-02_ses-002_task-mario3_run-01_part-phase_events.tsv => sub-02_ses-002_task-mario3_run-02_events.tsv} (100%) rename sub-02/ses-002/func/{sub-02_ses-002_task-mario3_run-02_part-mag_events.tsv => sub-02_ses-002_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_part-phase_events.tsv rename sub-02/ses-002/func/{sub-02_ses-002_task-mario3_run-02_part-phase_events.tsv => sub-02_ses-002_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_events.tsv similarity index 100% rename from sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-01_part-phase_events.tsv rename to sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_events.tsv diff --git a/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_part-mag_events.tsv b/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_events.tsv similarity index 100% rename from sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_part-mag_events.tsv rename to sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_events.tsv diff --git a/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_part-mag_events.tsv b/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_part-phase_events.tsv b/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_events.tsv similarity index 100% rename from sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_part-phase_events.tsv rename to sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_events.tsv diff --git a/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-mag_events.tsv b/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_events.tsv b/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From a9b8286eb095974ee0e3e812b426f96314ea0bcf Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:39:19 -0400 Subject: [PATCH 121/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-008_acq-axial_localizer.json | 81 +++ .../sub-02_ses-008_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-008_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-008_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-008_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-008_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-008/anat/sub-02_ses-008_scout.json | 542 ++++++++++++++++++ .../ses-008/anat/sub-02_ses-008_scout.nii.gz | 1 + ...8_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-008_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-01_part-mag_events.tsv | 1 + ...008_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-01_part-phase_events.tsv | 1 + ...8_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-008_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-02_part-mag_events.tsv | 1 + ...008_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-02_part-phase_events.tsv | 1 + ...8_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-008_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-03_part-mag_events.tsv | 1 + ...008_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-03_part-phase_events.tsv | 1 + ...8_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-008_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-04_part-mag_events.tsv | 1 + ...008_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-04_part-phase_events.tsv | 1 + ...8_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-02/ses-008/sub-02_ses-008_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5409 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-008/anat/sub-02_ses-008_acq-axial_localizer.json create mode 120000 sub-02/ses-008/anat/sub-02_ses-008_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-008/anat/sub-02_ses-008_acq-coronal_localizer.json create mode 120000 sub-02/ses-008/anat/sub-02_ses-008_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-008/anat/sub-02_ses-008_acq-sagittal_localizer.json create mode 120000 sub-02/ses-008/anat/sub-02_ses-008_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-008/anat/sub-02_ses-008_scout.json create mode 120000 sub-02/ses-008/anat/sub-02_ses-008_scout.nii.gz create mode 100644 sub-02/ses-008/fmap/sub-02_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-008/fmap/sub-02_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-008/fmap/sub-02_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-008/fmap/sub-02_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_part-phase_sbref.nii.gz create mode 120000 sub-02/ses-008/sub-02_ses-008_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index f45add5ab..96a41114c 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit f45add5abada864982269105c5c72daad8a0cffb +Subproject commit 96a41114c553003df42a38491a729d6e39b528a8 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..83ada7a9d --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 51 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-008/anat/sub-02_ses-008_acq-axial_localizer.json b/sub-02/ses-008/anat/sub-02_ses-008_acq-axial_localizer.json new file mode 100644 index 000000000..7343b2a98 --- /dev/null +++ b/sub-02/ses-008/anat/sub-02_ses-008_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:15:55.045000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0508122, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 306.038 +} \ No newline at end of file diff --git a/sub-02/ses-008/anat/sub-02_ses-008_acq-axial_localizer.nii.gz b/sub-02/ses-008/anat/sub-02_ses-008_acq-axial_localizer.nii.gz new file mode 120000 index 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"SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 306.038, + "dcmmeta_affine": [ + [-1.9976927042007446, 0.04742710664868355, 0.0835123285651207, 102.96373748779297], + [-0.005440785549581051, 1.6804389953613281, -1.0844790935516357, -47.641441345214844], + [0.09588554501533508, 1.083455204963684, 1.6783714294433594, -96.09222412109375], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 2ab9829bee32a36be099d3851d5fc561668e52fd Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:39:56 -0400 Subject: [PATCH 122/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-011_acq-axial_localizer.json | 81 +++ .../sub-02_ses-011_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-011_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-011_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-011_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-011_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-011/anat/sub-02_ses-011_scout.json | 542 ++++++++++++++++++ .../ses-011/anat/sub-02_ses-011_scout.nii.gz | 1 + ...1_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-011_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...11_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...011_task-mario3_run-01_part-mag_events.tsv | 1 + ...011_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...11_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-01_part-phase_events.tsv | 1 + ...1_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-011_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...11_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...011_task-mario3_run-02_part-mag_events.tsv | 1 + ...011_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...11_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-02_part-phase_events.tsv | 1 + ...1_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-011_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...11_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...011_task-mario3_run-03_part-mag_events.tsv | 1 + ...011_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...11_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-03_part-phase_events.tsv | 1 + ...1_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-011_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...11_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...011_task-mario3_run-04_part-mag_events.tsv | 1 + ...011_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...11_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-04_part-phase_events.tsv | 1 + ...1_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-02/ses-011/sub-02_ses-011_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5409 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-011/anat/sub-02_ses-011_acq-axial_localizer.json create mode 120000 sub-02/ses-011/anat/sub-02_ses-011_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-011/anat/sub-02_ses-011_acq-coronal_localizer.json create mode 120000 sub-02/ses-011/anat/sub-02_ses-011_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-011/anat/sub-02_ses-011_acq-sagittal_localizer.json create mode 120000 sub-02/ses-011/anat/sub-02_ses-011_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-011/anat/sub-02_ses-011_scout.json create mode 120000 sub-02/ses-011/anat/sub-02_ses-011_scout.nii.gz create mode 100644 sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_part-phase_sbref.nii.gz create mode 120000 sub-02/ses-011/sub-02_ses-011_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index def1d1689..7e7ba30a4 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit def1d1689d1cc283b8bab71f366ed9dec2d094b1 +Subproject commit 7e7ba30a46a2968081a4e1a0b815e2a38f5e6e18 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..83ada7a9d --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 51 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-011/anat/sub-02_ses-011_acq-axial_localizer.json b/sub-02/ses-011/anat/sub-02_ses-011_acq-axial_localizer.json new file mode 100644 index 000000000..89bf9e365 --- /dev/null +++ b/sub-02/ses-011/anat/sub-02_ses-011_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:15:30.035000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0312011, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 253.247 +} \ No newline at end of file diff --git a/sub-02/ses-011/anat/sub-02_ses-011_acq-axial_localizer.nii.gz b/sub-02/ses-011/anat/sub-02_ses-011_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..bd678f28f --- /dev/null +++ b/sub-02/ses-011/anat/sub-02_ses-011_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/jv/92/MD5E-s181752--9e039482269c439aa66b965514d14685.nii.gz/MD5E-s181752--9e039482269c439aa66b965514d14685.nii.gz \ No newline at end of file diff --git a/sub-02/ses-011/anat/sub-02_ses-011_acq-coronal_localizer.json b/sub-02/ses-011/anat/sub-02_ses-011_acq-coronal_localizer.json new file mode 100644 index 000000000..b78f61f4d --- /dev/null +++ b/sub-02/ses-011/anat/sub-02_ses-011_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:15:37.025000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + 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"N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999377, 0.00804827, 0.0343556, 0.0118614, 0.840356, -0.541905], + "ImageOrientationText": "Tra>Cor(-32.8)>Sag(1.9)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0459562, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [623, -7183, -8865, 241, 51, -189, -30, 57], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 253.247, + "dcmmeta_affine": [ + [-1.9987545013427734, 0.02372288703918457, 0.06646467745304108, 104.36060333251953], + [-0.016096536070108414, 1.680712342262268, -1.0839496850967407, -46.51134490966797], + [0.06871121376752853, 1.0838096141815186, 1.6794747114181519, -99.22900390625], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From e42454528988bca90bab8844725ae1724bd856bd Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:39:57 -0400 Subject: [PATCH 123/463] fix fmap phase --- ...2_ses-008_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-008_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-008_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-02/ses-008/sub-02_ses-008_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-02/ses-008/fmap/{sub-02_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-008_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-008/fmap/{sub-02_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-008_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-008/fmap/sub-02_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-008/fmap/sub-02_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-008/fmap/{sub-02_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-008_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-008/fmap/{sub-02_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-008_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-008/fmap/{sub-02_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-008_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-008/fmap/{sub-02_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-008_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-008/fmap/{sub-02_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-008_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-008/fmap/{sub-02_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-008_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-008/fmap/{sub-02_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-008_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-008/fmap/{sub-02_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-008_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-02/ses-008/fmap/{sub-02_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-02_ses-008_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-02/ses-008/fmap/{sub-02_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-02_ses-008_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-008/fmap/sub-02_ses-008_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-008/fmap/sub-02_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-008/fmap/sub-02_ses-008_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-008/fmap/sub-02_ses-008_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-008/fmap/sub-02_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-008/fmap/sub-02_ses-008_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-008/fmap/sub-02_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 559bf4317..000000000 --- a/sub-02/ses-008/fmap/sub-02_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:16:56.492500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.998846, 0.00272039, 0.0479428, 0.0237136, 0.840219, -0.541728], - "ImageOrientationText": 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0.05968627610523, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "111743.600000", - "SliceLocation": -50.506779244846, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999996612, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "111506.978000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["111656.492500", "111657.982500", "111659.472500"], - "ContentTime": ["111743.602000", "111743.605000", "111743.607000"], - "InstanceCreationTime": ["111743.602000", "111743.605000", "111743.607000"], - "InstanceNumber": [1, 2, 3], - 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sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 2848929bd..000000000 --- a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:16:46.062500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of 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b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index d6d847424..000000000 --- a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/z2/G3/MD5E-s1111936--7b6577685df9afc2d9d288908f746b99.nii.gz/MD5E-s1111936--7b6577685df9afc2d9d288908f746b99.nii.gz \ No newline at end of file diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index ee54a607a..000000000 --- a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:18:11.747500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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"PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0748414, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 625, - -7186, - -8866, - 220, - 32, - -201, - -44, - 41 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 306.038, - "WipMemBlock": "059eda4d-4dc5-49ed-b87b-1699f2d7d0d5||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index a78f63bc7..000000000 --- a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/mm/xp/MD5E-s1103390--8ed46ab283a7b757f1da50b9be81b2b3.nii.gz/MD5E-s1103390--8ed46ab283a7b757f1da50b9be81b2b3.nii.gz \ No newline at end of file diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index b75f29e88..000000000 --- a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:28:43.860000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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"%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0748414, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 625, - -7186, - -8866, - 220, - 32, - -201, - -44, - 41 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 306.038, - "WipMemBlock": "4515f2cf-e9c0-445c-a4c1-49f73e425a4a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index dfa9318bb..000000000 --- a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/kV/JJ/MD5E-s1103445--bd9ad6d192c641deeba6c17f5727554c.nii.gz/MD5E-s1103445--bd9ad6d192c641deeba6c17f5727554c.nii.gz \ No newline at end of file diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index f9b14bbf0..000000000 --- a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:37:29.157500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998846, - 0.00272039, - 0.0479428, - 0.0237136, - 0.840219, - -0.541728 - ], - "ImageOrientationText": "Tra>Cor(-32.9)>Sag(2.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0748414, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 625, - -7186, - -8866, - 220, - 32, - -201, - -44, - 41 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 306.038, - "WipMemBlock": "f60a4bce-c57a-438e-8a5d-c66fbf7b3126||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index b7310e933..000000000 --- a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/69/Wx/MD5E-s1103339--42fb86dcbf4ddd662affeef153fa0317.nii.gz/MD5E-s1103339--42fb86dcbf4ddd662affeef153fa0317.nii.gz \ No newline at end of file diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 9a5d9451d..000000000 --- a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:46:22.572500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998846, - 0.00272039, - 0.0479428, - 0.0237136, - 0.840219, - -0.541728 - ], - "ImageOrientationText": "Tra>Cor(-32.9)>Sag(2.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0748414, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 625, - -7186, - -8866, - 220, - 32, - -201, - -44, - 41 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 306.038, - "WipMemBlock": "2b2322e9-e158-4643-b8b6-f37208601bc4||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 9a5a43ce7..000000000 --- a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Wq/q2/MD5E-s1103261--28ec4fe18f1fe48106a6ed42f43c0410.nii.gz/MD5E-s1103261--28ec4fe18f1fe48106a6ed42f43c0410.nii.gz \ No newline at end of file diff --git a/sub-02/ses-008/sub-02_ses-008_scans.tsv b/sub-02/ses-008/sub-02_ses-008_scans.tsv index a5e736e4c..44e6e3528 120000 --- a/sub-02/ses-008/sub-02_ses-008_scans.tsv +++ b/sub-02/ses-008/sub-02_ses-008_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/mK/MX/MD5E-s3289--03a80276767cd1a833a3002a0cc649c4.tsv/MD5E-s3289--03a80276767cd1a833a3002a0cc649c4.tsv \ No newline at end of file +../../.git/annex/objects/V0/jv/MD5E-s2567--6eb27a2b51b5bc23c552637aa084175b.tsv/MD5E-s2567--6eb27a2b51b5bc23c552637aa084175b.tsv \ No newline at end of file From 9b69f6c1076d7c449a49690b0aa2a6e861294642 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:39:58 -0400 Subject: [PATCH 124/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-011_acq-axial_localizer.json | 81 +++ .../sub-01_ses-011_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-011_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-011_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-011_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-011_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-011/anat/sub-01_ses-011_scout.json | 542 ++++++++++++++++++ .../ses-011/anat/sub-01_ses-011_scout.nii.gz | 1 + ...1_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ...-011_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...11_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...011_task-mario3_run-01_part-mag_events.tsv | 1 + ...011_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...11_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-01_part-phase_events.tsv | 1 + ...1_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-011_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...11_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...011_task-mario3_run-02_part-mag_events.tsv | 1 + ...011_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...11_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-02_part-phase_events.tsv | 1 + ...1_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-011_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...11_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...011_task-mario3_run-03_part-mag_events.tsv | 1 + ...011_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...11_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-03_part-phase_events.tsv | 1 + ...1_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-011_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...11_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...011_task-mario3_run-04_part-mag_events.tsv | 1 + ...011_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...11_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-04_part-phase_events.tsv | 1 + ...1_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-011_task-mario3_run-05_part-mag_bold.json | 172 ++++++ ...11_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...011_task-mario3_run-05_part-mag_events.tsv | 1 + ...011_task-mario3_run-05_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...11_task-mario3_run-05_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-05_part-phase_events.tsv | 1 + ...1_task-mario3_run-05_part-phase_sbref.json | 153 +++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + sub-01/ses-011/sub-01_ses-011_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 93 files changed, 6371 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-011/anat/sub-01_ses-011_acq-axial_localizer.json create mode 120000 sub-01/ses-011/anat/sub-01_ses-011_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-011/anat/sub-01_ses-011_acq-coronal_localizer.json create mode 120000 sub-01/ses-011/anat/sub-01_ses-011_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-011/anat/sub-01_ses-011_acq-sagittal_localizer.json create mode 120000 sub-01/ses-011/anat/sub-01_ses-011_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-011/anat/sub-01_ses-011_scout.json create mode 120000 sub-01/ses-011/anat/sub-01_ses-011_scout.nii.gz create mode 100644 sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 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sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_part-mag_epi.json create mode 120000 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz create mode 100644 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_part-phase_epi.json create mode 120000 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz create mode 100644 sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-01_part-mag_events.tsv create mode 100644 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a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-011/anat/sub-01_ses-011_acq-axial_localizer.json b/sub-01/ses-011/anat/sub-01_ses-011_acq-axial_localizer.json new file mode 100644 index 000000000..616532274 --- /dev/null +++ b/sub-01/ses-011/anat/sub-01_ses-011_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:09:1.015000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + 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@@ -0,0 +1 @@ +../../../.git/annex/objects/k4/pM/MD5E-s353024065--5d37d9ff6208b865a4ae946242070441.nii.gz/MD5E-s353024065--5d37d9ff6208b865a4ae946242070441.nii.gz \ No newline at end of file diff --git a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_part-phase_events.tsv b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_part-phase_events.tsv new file mode 120000 index 000000000..1bbdfddb5 --- /dev/null +++ b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_part-phase_events.tsv @@ -0,0 +1 @@ +../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_part-phase_sbref.json b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_part-phase_sbref.json new file mode 100644 index 000000000..45492ad0e --- /dev/null +++ b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_part-phase_sbref.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:53:15.727500", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTime1": 0.037, + "EchoTime2": 0.001, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Single-band reference", + "ImageOrientationPatientDICOM": [ + 0.996278, + 0.0842897, + 0.018012, + -0.0745609, + 0.947641, + -0.310512 + ], + "ImageOrientationText": "Tra>Cor(-18.0)>Sag(2.5)", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "P", + "ND", + "MOSAIC", + "PHASE" + ], + 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"bbce273d-5ba9-46e2-926b-8baad8f8d3cf||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_part-phase_sbref.nii.gz b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_part-phase_sbref.nii.gz new file mode 120000 index 000000000..1f2e2bf2e --- /dev/null +++ b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/8W/0x/MD5E-s1103689--1c52a8c0c813cb8f5aa8beb6879325b4.nii.gz/MD5E-s1103689--1c52a8c0c813cb8f5aa8beb6879325b4.nii.gz \ No newline at end of file diff --git a/sub-01/ses-011/sub-01_ses-011_scans.tsv b/sub-01/ses-011/sub-01_ses-011_scans.tsv new file mode 120000 index 000000000..3cc98d95b --- /dev/null +++ b/sub-01/ses-011/sub-01_ses-011_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/Zk/J7/MD5E-s3911--919c0e959ae694e0e9ff805bdd319018.tsv/MD5E-s3911--919c0e959ae694e0e9ff805bdd319018.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..406eef5dc --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.996278, 0.0842897, 0.018012, -0.0745609, 0.947641, -0.310512], + "ImageOrientationText": "Tra>Cor(-18.0)>Sag(2.5)", + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0485791, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [622, -7196, -8826, 661, 122, 44, -47, 13], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 255.023, + "dcmmeta_affine": [ + [-1.9925569295883179, -0.1491217464208603, 0.0864836722612381, 110.60840606689453], + [-0.1685793548822403, 1.895281434059143, -0.6160269379615784, -54.754844665527344], + [0.03602394089102745, 0.6210240721702576, 1.9007974863052368, -61.78437805175781], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From f33c3daed5ff0efc8dac194fff8bc27664ee4722 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:40:01 -0400 Subject: [PATCH 125/463] fill IntendedFor --- ...2_ses-002_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...2_ses-002_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...2_ses-002_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...2_ses-002_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...2_ses-002_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_epi.json index 9ff7bfb94..abaea3d0e 100644 --- a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998714, - 0.00370923, - 0.0505703, - 0.0231871, - 0.85353, - -0.520527 - ], + "ImageOrientationPatientDICOM": [0.998714, 0.00370923, 0.0505703, 0.0231871, 0.85353, -0.520527], "ImageOrientationText": "Tra>Cor(-31.4)>Sag(2.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-02_ses-002_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-002/func/sub-02_ses-002_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-002/func/sub-02_ses-002_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-002/func/sub-02_ses-002_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 624, - -7178, - -8864, - 275, - 44, - -177, - -50, - 17 - ], + "ShimSetting": [624, -7178, -8864, 275, 44, -177, -50, 17], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_epi.json b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_epi.json index 8648449e7..bfd4032a3 100644 --- a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998714, - 0.00370923, - 0.0505703, - 0.0231871, - 0.85353, - -0.520527 - ], + "ImageOrientationPatientDICOM": [0.998714, 0.00370923, 0.0505703, 0.0231871, 0.85353, -0.520527], "ImageOrientationText": "Tra>Cor(-31.4)>Sag(2.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-02_ses-002_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 624, - -7178, - -8864, - 275, - 44, - -177, - -50, - 17 - ], + "ShimSetting": [624, -7178, -8864, 275, 44, -177, -50, 17], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_epi.json b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_epi.json index 0f8974a0e..0d9c3dcea 100644 --- a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998714, - 0.00370923, - 0.0505703, - 0.0231871, - 0.85353, - -0.520527 - ], + "ImageOrientationPatientDICOM": [0.998714, 0.00370923, 0.0505703, 0.0231871, 0.85353, -0.520527], "ImageOrientationText": "Tra>Cor(-31.4)>Sag(2.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-02_ses-002_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 624, - -7178, - -8864, - 275, - 44, - -177, - -50, - 17 - ], + "ShimSetting": [624, -7178, -8864, 275, 44, -177, -50, 17], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_epi.json b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_epi.json index 5c5bada88..d2139cc75 100644 --- a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998714, - 0.00370923, - 0.0505703, - 0.0231871, - 0.85353, - -0.520527 - ], + "ImageOrientationPatientDICOM": [0.998714, 0.00370923, 0.0505703, 0.0231871, 0.85353, -0.520527], "ImageOrientationText": "Tra>Cor(-31.4)>Sag(2.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-02_ses-002_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 624, - -7178, - -8864, - 275, - 44, - -177, - -50, - 17 - ], + "ShimSetting": [624, -7178, -8864, 275, 44, -177, -50, 17], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_epi.json b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_epi.json index d77b7157c..02e199f9a 100644 --- a/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-02/ses-002/fmap/sub-02_ses-002_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998714, - 0.00370923, - 0.0505703, - 0.0231871, - 0.85353, - -0.520527 - ], + "ImageOrientationPatientDICOM": [0.998714, 0.00370923, 0.0505703, 0.0231871, 0.85353, -0.520527], "ImageOrientationText": "Tra>Cor(-31.4)>Sag(2.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-02_ses-002_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 624, - -7178, - -8864, - 275, - 44, - -177, - -50, - 17 - ], + "ShimSetting": [624, -7178, -8864, 275, 44, -177, -50, 17], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 9a578ce7e060ebe6b9b717c2845f03088da0a890 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:40:04 -0400 Subject: [PATCH 126/463] fix complex event files --- ...g_events.tsv => sub-02_ses-008_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-02_ses-008_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-02_ses-008_task-mario3_run-03_events.tsv} | 0 .../func/sub-02_ses-008_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-02_ses-008_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-02_ses-008_task-mario3_run-04_events.tsv} | 0 .../func/sub-02_ses-008_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-02_ses-008_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-02/ses-008/func/{sub-02_ses-008_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-008_task-mario3_run-01_events.tsv} (100%) rename sub-02/ses-008/func/{sub-02_ses-008_task-mario3_run-01_part-phase_events.tsv => sub-02_ses-008_task-mario3_run-02_events.tsv} (100%) rename sub-02/ses-008/func/{sub-02_ses-008_task-mario3_run-02_part-mag_events.tsv => sub-02_ses-008_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_part-phase_events.tsv rename sub-02/ses-008/func/{sub-02_ses-008_task-mario3_run-02_part-phase_events.tsv => sub-02_ses-008_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-02_events.tsv similarity index 100% rename from sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-01_part-phase_events.tsv rename to sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-02_events.tsv diff --git a/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-02_part-mag_events.tsv b/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_events.tsv similarity index 100% rename from sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-02_part-mag_events.tsv rename to sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_events.tsv diff --git a/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_part-mag_events.tsv b/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-02_part-phase_events.tsv b/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_events.tsv similarity index 100% rename from sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-02_part-phase_events.tsv rename to sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_events.tsv diff --git a/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_part-mag_events.tsv b/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_part-phase_events.tsv b/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-008/func/sub-02_ses-008_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 243e379a5cab5ee0c144f686be94cbb3f63ec77b Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:40:34 -0400 Subject: [PATCH 127/463] fix fmap phase --- ...2_ses-011_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-011_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-011_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-011_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-011_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-011_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-011_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-02/ses-011/sub-02_ses-011_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-02/ses-011/fmap/{sub-02_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-011_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-011/fmap/{sub-02_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-011_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-011/fmap/{sub-02_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-011_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-011/fmap/{sub-02_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-011_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-011/fmap/{sub-02_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-011_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-011/fmap/{sub-02_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-011_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-011/fmap/{sub-02_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-011_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-011/fmap/{sub-02_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-011_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-011/fmap/{sub-02_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-011_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-011/fmap/{sub-02_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-011_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-02/ses-011/fmap/{sub-02_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-02_ses-011_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-02/ses-011/fmap/{sub-02_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-02_ses-011_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index bf5856ade..000000000 --- a/sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:16:30.227500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999377, 0.00804827, 0.0343556, 0.0118614, 0.840356, -0.541905], - "ImageOrientationText": "Tra>Cor(-32.8)>Sag(1.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0366502, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [623, -7183, -8865, 241, 51, -189, -30, 57], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.0975, 0.8825, 0.195, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685, 0, 0.785, 0.0975, 0.8825, 0.195, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685, 0, 0.785, 0.0975, 0.8825, 0.195, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685, 0, 0.785, 0.0975, 0.8825, 0.195, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 253.247, - "WipMemBlock": "b1fcc733-a810-47aa-b177-8347e2a9d2a7||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9987545013427734, 0.02372288703918457, 0.06646467745304108, 104.36060333251953], - [-0.016096536070108414, 1.680712342262268, -1.0839496850967407, -46.51134490966797], - [0.06871121376752853, 1.0838096141815186, 1.6794747114181519, -99.22900390625], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99937726495264, 0.00804826761684, 0.03435560629863, 0.01186144341528, 0.84035616637028, -0.5419048069574], - "ImagePositionPatient": [-842.98583804911, -744.24045477553, 381.89920200743], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.258974, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "161444.850000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.03665023790715, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "161715.881000", - "SliceLocation": -54.650180623133, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999683453, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "161444.763000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["161630.227500", "161631.717500", "161633.207500"], - "ContentTime": ["161715.883000", "161715.886000", "161715.888000"], - "InstanceCreationTime": ["161715.883000", "161715.886000", "161715.888000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4770.0, 4776.0, 4772.0], - "WindowWidth": [18500.0, 18500.0, 18504.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index c15b4bb29..000000000 --- a/sub-02/ses-011/fmap/sub-02_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/PZ/z1/MD5E-s3333440--831c5086fd686a17e02bacef50bd2bc9.nii.gz/MD5E-s3333440--831c5086fd686a17e02bacef50bd2bc9.nii.gz \ No newline at end of file diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 158d658d0..000000000 --- a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:16:19.797500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999377, - 0.00804827, - 0.0343556, - 0.0118614, - 0.840356, - -0.541905 - ], - "ImageOrientationText": "Tra>Cor(-32.8)>Sag(1.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0366502, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 623, - -7183, - -8865, - 241, - 51, - -189, - -30, - 57 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 253.247, - "WipMemBlock": "b1fcc733-a810-47aa-b177-8347e2a9d2a7||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 80a59cf67..000000000 --- a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/G2/x0/MD5E-s1112055--d486a28571b072ba9f3d274d852bd0c3.nii.gz/MD5E-s1112055--d486a28571b072ba9f3d274d852bd0c3.nii.gz \ No newline at end of file diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index d92ab2bcb..000000000 --- a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:17:37.127500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999377, - 0.00804827, - 0.0343556, - 0.0118614, - 0.840356, - -0.541905 - ], - "ImageOrientationText": "Tra>Cor(-32.8)>Sag(1.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0459562, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 623, - -7183, - -8865, - 241, - 51, - -189, - -30, - 57 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 253.247, - "WipMemBlock": "47b0aecd-0dd8-4a9c-871d-037008611d9f||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 26f9324f6..000000000 --- a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/6V/XG/MD5E-s1103326--e56bd4fa5dce17655814434aa5d58afd.nii.gz/MD5E-s1103326--e56bd4fa5dce17655814434aa5d58afd.nii.gz \ No newline at end of file diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index aad129011..000000000 --- a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:26:49.890000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999377, - 0.00804827, - 0.0343556, - 0.0118614, - 0.840356, - -0.541905 - ], - "ImageOrientationText": "Tra>Cor(-32.8)>Sag(1.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0459562, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 623, - -7183, - -8865, - 241, - 51, - -189, - -30, - 57 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 253.247, - "WipMemBlock": "b336d778-5861-4f4a-99d8-1c8eb5572c81||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 37e803520..000000000 --- a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Pf/Gk/MD5E-s1103289--6ac51b61c85616485aad45f650ce3a4f.nii.gz/MD5E-s1103289--6ac51b61c85616485aad45f650ce3a4f.nii.gz \ No newline at end of file diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 9e54b0dd0..000000000 --- a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:39:55.460000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999377, - 0.00804827, - 0.0343556, - 0.0118614, - 0.840356, - -0.541905 - ], - "ImageOrientationText": "Tra>Cor(-32.8)>Sag(1.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0459562, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 623, - -7183, - -8865, - 241, - 51, - -189, - -30, - 57 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 253.247, - "WipMemBlock": "22103e83-aa8b-479f-813a-377ece023dfd||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 7b142c0d2..000000000 --- a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/WQ/X4/MD5E-s1103111--a94926efb56f69b5b2313b115f7b074f.nii.gz/MD5E-s1103111--a94926efb56f69b5b2313b115f7b074f.nii.gz \ No newline at end of file diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index a3c182884..000000000 --- a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:48:7.927500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999377, - 0.00804827, - 0.0343556, - 0.0118614, - 0.840356, - -0.541905 - ], - "ImageOrientationText": "Tra>Cor(-32.8)>Sag(1.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0459562, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 623, - -7183, - -8865, - 241, - 51, - -189, - -30, - 57 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 253.247, - "WipMemBlock": "9eafadc9-d83b-424a-a84e-0f3e404df803||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 6e051964d..000000000 --- a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/1W/JM/MD5E-s1103507--43a09146414c0f6952606da5e6321ee6.nii.gz/MD5E-s1103507--43a09146414c0f6952606da5e6321ee6.nii.gz \ No newline at end of file diff --git a/sub-02/ses-011/sub-02_ses-011_scans.tsv b/sub-02/ses-011/sub-02_ses-011_scans.tsv index 15f06caab..0238569c6 120000 --- a/sub-02/ses-011/sub-02_ses-011_scans.tsv +++ b/sub-02/ses-011/sub-02_ses-011_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/zF/5M/MD5E-s3289--006e646fc083f92f468704c3dc640d0e.tsv/MD5E-s3289--006e646fc083f92f468704c3dc640d0e.tsv \ No newline at end of file +../../.git/annex/objects/3j/mV/MD5E-s2567--1198eeae9de0bd0862ba8e5ea11988c6.tsv/MD5E-s2567--1198eeae9de0bd0862ba8e5ea11988c6.tsv \ No newline at end of file From 2c67bd4aafa10bbb58ade1b401b2f0a1faad4abb Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:40:38 -0400 Subject: [PATCH 128/463] fix fmap phase --- ...1_ses-011_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-011_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-011_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-011_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-011_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-011_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-011_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-011_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - sub-01/ses-011/sub-01_ses-011_scans.tsv | 2 +- 29 files changed, 1 insertion(+), 1097 deletions(-) rename sub-01/ses-011/fmap/{sub-01_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-011_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-011/fmap/{sub-01_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-011_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-011/fmap/{sub-01_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-011_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-011/fmap/{sub-01_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-011_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-011/fmap/{sub-01_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-011_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-011/fmap/{sub-01_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-011_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-011/fmap/{sub-01_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-011_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-011/fmap/{sub-01_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-011_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-01/ses-011/fmap/{sub-01_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-01_ses-011_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-01/ses-011/fmap/{sub-01_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-01_ses-011_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-01/ses-011/fmap/{sub-01_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-01_ses-011_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-01/ses-011/fmap/{sub-01_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-01_ses-011_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-01/ses-011/fmap/{sub-01_ses-011_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-01_ses-011_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-01/ses-011/fmap/{sub-01_ses-011_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-01_ses-011_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index f8f7a84b4..000000000 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:10:6.047500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.996278, 0.0842897, 0.018012, -0.0745609, 0.947641, -0.310512], - "ImageOrientationText": "Tra>Cor(-18.0)>Sag(2.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.038742, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [622, -7196, -8826, 661, 122, 44, -47, 13], - "SliceThickness": 2, - "SliceTiming": [0, 0.7825, 0.0975, 0.88, 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[ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99627848500032, 0.0842896746141, 0.01801197043424, -0.074560874287, 0.94764072753544, -0.3105120408964], - "ImagePositionPatient": [-766.25928592822, -891.70447654643, 215.12115367155], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.260307, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": 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"SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "110812.190000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["111006.047500", "111007.537500", "111009.027500"], - "ContentTime": ["111052.148000", "111052.151000", "111052.154000"], - "InstanceCreationTime": ["111052.148000", "111052.151000", "111052.154000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4774.0, 4776.0, 4772.0], - "WindowWidth": [18574.0, 18574.0, 18570.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index f2898ad94..000000000 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/8G/1G/MD5E-s3335044--088a80cb0715eb03df46e0e2b3b70e06.nii.gz/MD5E-s3335044--088a80cb0715eb03df46e0e2b3b70e06.nii.gz \ No newline at end of file diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index d2a25c1b5..000000000 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:09:55.617500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996278, - 0.0842897, - 0.018012, - -0.0745609, - 0.947641, - -0.310512 - ], - "ImageOrientationText": "Tra>Cor(-18.0)>Sag(2.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.038742, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 622, - -7196, - -8826, - 661, - 122, - 44, - -47, - 13 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 255.023, - "WipMemBlock": "e04688df-0405-491f-956d-e8f52e3fc5c1||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 4483ec5cf..000000000 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/V1/5Z/MD5E-s1112306--420e47a5ca57a2026321044402581e08.nii.gz/MD5E-s1112306--420e47a5ca57a2026321044402581e08.nii.gz \ No newline at end of file diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index b11dcf447..000000000 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:11:4.402500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996278, - 0.0842897, - 0.018012, - -0.0745609, - 0.947641, - -0.310512 - ], - "ImageOrientationText": "Tra>Cor(-18.0)>Sag(2.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - 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"2f929cfa-6457-4adc-8f27-630301dced2c||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 7a4b9d2f4..000000000 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/54/16/MD5E-s1103773--009e3b077c8a9fec0f6953097d0ae3ab.nii.gz/MD5E-s1103773--009e3b077c8a9fec0f6953097d0ae3ab.nii.gz \ No newline at end of file diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 139d326bb..000000000 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:20:38.070000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of 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b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 82544a7bb..000000000 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/1q/pP/MD5E-s1103865--51d5b72c8440280486aacbc03e201cd4.nii.gz/MD5E-s1103865--51d5b72c8440280486aacbc03e201cd4.nii.gz \ No newline at end of file diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 7e3afd91f..000000000 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:31:43.882500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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"PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0485791, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 622, - -7196, - -8826, - 661, - 122, - 44, - -47, - 13 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 255.023, - "WipMemBlock": "dd3b3cef-f524-42bf-932f-9152d1a77f45||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 686c9ed00..000000000 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/kx/86/MD5E-s1103821--452180dd73419374a8c93f4d960516e1.nii.gz/MD5E-s1103821--452180dd73419374a8c93f4d960516e1.nii.gz \ No newline at end of file diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index fb6e03cdb..000000000 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:41:19.330000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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"%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0485791, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 622, - -7196, - -8826, - 661, - 122, - 44, - -47, - 13 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 255.023, - "WipMemBlock": "fbe5788b-021a-4cfc-883e-2f72e8a73167||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 395ddff51..000000000 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/4k/Pw/MD5E-s1103854--264f7d836cafb3a2f09643cb7d64f229.nii.gz/MD5E-s1103854--264f7d836cafb3a2f09643cb7d64f229.nii.gz \ No newline at end of file diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index bd909e3c3..000000000 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:53:15.727500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996278, - 0.0842897, - 0.018012, - -0.0745609, - 0.947641, - -0.310512 - ], - "ImageOrientationText": "Tra>Cor(-18.0)>Sag(2.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-05", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0485791, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 622, - -7196, - -8826, - 661, - 122, - 44, - -47, - 13 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 255.023, - "WipMemBlock": "bbce273d-5ba9-46e2-926b-8baad8f8d3cf||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index 1f2e2bf2e..000000000 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/8W/0x/MD5E-s1103689--1c52a8c0c813cb8f5aa8beb6879325b4.nii.gz/MD5E-s1103689--1c52a8c0c813cb8f5aa8beb6879325b4.nii.gz \ No newline at end of file diff --git a/sub-01/ses-011/sub-01_ses-011_scans.tsv b/sub-01/ses-011/sub-01_ses-011_scans.tsv index 3cc98d95b..24a983adc 120000 --- a/sub-01/ses-011/sub-01_ses-011_scans.tsv +++ b/sub-01/ses-011/sub-01_ses-011_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/Zk/J7/MD5E-s3911--919c0e959ae694e0e9ff805bdd319018.tsv/MD5E-s3911--919c0e959ae694e0e9ff805bdd319018.tsv \ No newline at end of file +../../.git/annex/objects/mw/FF/MD5E-s3068--d1996aeb4d89728de46af8dc0a75e811.tsv/MD5E-s3068--d1996aeb4d89728de46af8dc0a75e811.tsv \ No newline at end of file From ddfdd8699f1cc4d38b4915fa0c7765ef45ee45f0 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:40:45 -0400 Subject: [PATCH 129/463] fix complex event files --- ...g_events.tsv => sub-02_ses-011_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-02_ses-011_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-02_ses-011_task-mario3_run-03_events.tsv} | 0 .../func/sub-02_ses-011_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-02_ses-011_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-02_ses-011_task-mario3_run-04_events.tsv} | 0 .../func/sub-02_ses-011_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-02_ses-011_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-02/ses-011/func/{sub-02_ses-011_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-011_task-mario3_run-01_events.tsv} (100%) rename sub-02/ses-011/func/{sub-02_ses-011_task-mario3_run-01_part-phase_events.tsv => sub-02_ses-011_task-mario3_run-02_events.tsv} (100%) rename sub-02/ses-011/func/{sub-02_ses-011_task-mario3_run-02_part-mag_events.tsv => sub-02_ses-011_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_part-phase_events.tsv rename sub-02/ses-011/func/{sub-02_ses-011_task-mario3_run-02_part-phase_events.tsv => sub-02_ses-011_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-02_events.tsv similarity index 100% rename from sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-01_part-phase_events.tsv rename to sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-02_events.tsv diff --git a/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-02_part-mag_events.tsv b/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_events.tsv similarity index 100% rename from sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-02_part-mag_events.tsv rename to sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_events.tsv diff --git a/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_part-mag_events.tsv b/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-02_part-phase_events.tsv b/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_events.tsv similarity index 100% rename from sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-02_part-phase_events.tsv rename to sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_events.tsv diff --git a/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_part-mag_events.tsv b/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_part-phase_events.tsv b/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-011/func/sub-02_ses-011_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 92ab8a4e05c2b2451fc1755278de7179923feb07 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:40:48 -0400 Subject: [PATCH 130/463] fix complex event files --- ...g_events.tsv => sub-01_ses-011_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-011_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-01_ses-011_task-mario3_run-03_events.tsv} | 0 .../func/sub-01_ses-011_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-01_ses-011_task-mario3_run-04_events.tsv} | 0 .../func/sub-01_ses-011_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-01_ses-011_task-mario3_run-04_part-phase_events.tsv | 1 - ...g_events.tsv => sub-01_ses-011_task-mario3_run-05_events.tsv} | 0 .../func/sub-01_ses-011_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-01_ses-011_task-mario3_run-05_part-phase_events.tsv | 1 - 10 files changed, 5 deletions(-) rename sub-01/ses-011/func/{sub-01_ses-011_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-011_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-011/func/{sub-01_ses-011_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-011_task-mario3_run-02_events.tsv} (100%) rename sub-01/ses-011/func/{sub-01_ses-011_task-mario3_run-02_part-mag_events.tsv => sub-01_ses-011_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-03_part-phase_events.tsv rename sub-01/ses-011/func/{sub-01_ses-011_task-mario3_run-02_part-phase_events.tsv => sub-01_ses-011_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-04_part-phase_events.tsv rename sub-01/ses-011/func/{sub-01_ses-011_task-mario3_run-03_part-mag_events.tsv => sub-01_ses-011_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_part-phase_events.tsv diff --git a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-03_events.tsv similarity index 100% rename from sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-02_part-mag_events.tsv rename to sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-03_events.tsv diff --git a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-04_events.tsv similarity index 100% rename from sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-02_part-phase_events.tsv rename to sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-04_events.tsv diff --git a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-04_part-mag_events.tsv b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-04_part-phase_events.tsv b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-03_part-mag_events.tsv b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_events.tsv similarity index 100% rename from sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-03_part-mag_events.tsv rename to sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_events.tsv diff --git a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_part-mag_events.tsv b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_part-phase_events.tsv b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 4d5ea0eef1168d8084cdbed407d1272050fb5a07 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:40:54 -0400 Subject: [PATCH 131/463] fill IntendedFor --- ...2_ses-008_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...2_ses-008_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...2_ses-008_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...2_ses-008_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...2_ses-008_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_epi.json index c3cae46b9..e2a2c96be 100644 --- a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998846, - 0.00272039, - 0.0479428, - 0.0237136, - 0.840219, - -0.541728 - ], + "ImageOrientationPatientDICOM": [0.998846, 0.00272039, 0.0479428, 0.0237136, 0.840219, -0.541728], "ImageOrientationText": "Tra>Cor(-32.9)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-02_ses-008_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-008/func/sub-02_ses-008_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-008/func/sub-02_ses-008_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-008/func/sub-02_ses-008_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 625, - -7186, - -8866, - 220, - 32, - -201, - -44, - 41 - ], + "ShimSetting": [625, -7186, -8866, 220, 32, -201, -44, 41], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_epi.json b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_epi.json index ca0f9fab9..d1b9381d2 100644 --- a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998846, - 0.00272039, - 0.0479428, - 0.0237136, - 0.840219, - -0.541728 - ], + "ImageOrientationPatientDICOM": [0.998846, 0.00272039, 0.0479428, 0.0237136, 0.840219, -0.541728], "ImageOrientationText": "Tra>Cor(-32.9)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-02_ses-008_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 625, - -7186, - -8866, - 220, - 32, - -201, - -44, - 41 - ], + "ShimSetting": [625, -7186, -8866, 220, 32, -201, -44, 41], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_epi.json b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_epi.json index bfd12e183..084125758 100644 --- a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998846, - 0.00272039, - 0.0479428, - 0.0237136, - 0.840219, - -0.541728 - ], + "ImageOrientationPatientDICOM": [0.998846, 0.00272039, 0.0479428, 0.0237136, 0.840219, -0.541728], "ImageOrientationText": "Tra>Cor(-32.9)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-02_ses-008_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 625, - -7186, - -8866, - 220, - 32, - -201, - -44, - 41 - ], + "ShimSetting": [625, -7186, -8866, 220, 32, -201, -44, 41], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_epi.json b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_epi.json index 88b5eb6b2..065093ce2 100644 --- a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998846, - 0.00272039, - 0.0479428, - 0.0237136, - 0.840219, - -0.541728 - ], + "ImageOrientationPatientDICOM": [0.998846, 0.00272039, 0.0479428, 0.0237136, 0.840219, -0.541728], "ImageOrientationText": "Tra>Cor(-32.9)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-02_ses-008_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 625, - -7186, - -8866, - 220, - 32, - -201, - -44, - 41 - ], + "ShimSetting": [625, -7186, -8866, 220, 32, -201, -44, 41], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.02, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_epi.json b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_epi.json index b623ee6bb..11b4d32ab 100644 --- a/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-02/ses-008/fmap/sub-02_ses-008_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998846, - 0.00272039, - 0.0479428, - 0.0237136, - 0.840219, - -0.541728 - ], + "ImageOrientationPatientDICOM": [0.998846, 0.00272039, 0.0479428, 0.0237136, 0.840219, -0.541728], "ImageOrientationText": "Tra>Cor(-32.9)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-02_ses-008_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 625, - -7186, - -8866, - 220, - 32, - -201, - -44, - 41 - ], + "ShimSetting": [625, -7186, -8866, 220, 32, -201, -44, 41], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From fbbb7993c40253894019da05369236d4a0d92132 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:41:44 -0400 Subject: [PATCH 132/463] fill IntendedFor --- ...2_ses-011_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...2_ses-011_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...2_ses-011_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...2_ses-011_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...2_ses-011_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_epi.json index d106365d2..9a7e0b0df 100644 --- a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999377, - 0.00804827, - 0.0343556, - 0.0118614, - 0.840356, - -0.541905 - ], + "ImageOrientationPatientDICOM": [0.999377, 0.00804827, 0.0343556, 0.0118614, 0.840356, -0.541905], "ImageOrientationText": "Tra>Cor(-32.8)>Sag(1.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-02_ses-011_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-011/func/sub-02_ses-011_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-011/func/sub-02_ses-011_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-011/func/sub-02_ses-011_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 623, - -7183, - -8865, - 241, - 51, - -189, - -30, - 57 - ], + "ShimSetting": [623, -7183, -8865, 241, 51, -189, -30, 57], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_epi.json b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_epi.json index 1d020d178..79b14000c 100644 --- a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999377, - 0.00804827, - 0.0343556, - 0.0118614, - 0.840356, - -0.541905 - ], + "ImageOrientationPatientDICOM": [0.999377, 0.00804827, 0.0343556, 0.0118614, 0.840356, -0.541905], "ImageOrientationText": "Tra>Cor(-32.8)>Sag(1.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-02_ses-011_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 623, - -7183, - -8865, - 241, - 51, - -189, - -30, - 57 - ], + "ShimSetting": [623, -7183, -8865, 241, 51, -189, -30, 57], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_epi.json b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_epi.json index da2b59da2..acdaaa213 100644 --- a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999377, - 0.00804827, - 0.0343556, - 0.0118614, - 0.840356, - -0.541905 - ], + "ImageOrientationPatientDICOM": [0.999377, 0.00804827, 0.0343556, 0.0118614, 0.840356, -0.541905], "ImageOrientationText": "Tra>Cor(-32.8)>Sag(1.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-02_ses-011_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 623, - -7183, - -8865, - 241, - 51, - -189, - -30, - 57 - ], + "ShimSetting": [623, -7183, -8865, 241, 51, -189, -30, 57], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_epi.json b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_epi.json index af2312c2a..ab6570b92 100644 --- a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999377, - 0.00804827, - 0.0343556, - 0.0118614, - 0.840356, - -0.541905 - ], + "ImageOrientationPatientDICOM": [0.999377, 0.00804827, 0.0343556, 0.0118614, 0.840356, -0.541905], "ImageOrientationText": "Tra>Cor(-32.8)>Sag(1.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-02_ses-011_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 623, - -7183, - -8865, - 241, - 51, - -189, - -30, - 57 - ], + "ShimSetting": [623, -7183, -8865, 241, 51, -189, -30, 57], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_epi.json b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_epi.json index 88eb09065..899aebec8 100644 --- a/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-02/ses-011/fmap/sub-02_ses-011_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999377, - 0.00804827, - 0.0343556, - 0.0118614, - 0.840356, - -0.541905 - ], + "ImageOrientationPatientDICOM": [0.999377, 0.00804827, 0.0343556, 0.0118614, 0.840356, -0.541905], "ImageOrientationText": "Tra>Cor(-32.8)>Sag(1.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-02_ses-011_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 623, - -7183, - -8865, - 241, - 51, - -189, - -30, - 57 - ], + "ShimSetting": [623, -7183, -8865, 241, 51, -189, -30, 57], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 0b7b046826d839d2ac6b149047f9a375abaa8b53 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:41:50 -0400 Subject: [PATCH 133/463] fill IntendedFor --- ...1_ses-011_acq-sbref_dir-AP_run-01_epi.json | 92 +++---------------- ...1_ses-011_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-011_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...1_ses-011_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...1_ses-011_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- ...1_ses-011_acq-sbref_dir-PA_run-05_epi.json | 88 ++---------------- 6 files changed, 46 insertions(+), 486 deletions(-) diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_epi.json index 823375e21..bada29995 100644 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996278, - 0.0842897, - 0.018012, - -0.0745609, - 0.947641, - -0.310512 - ], + "ImageOrientationPatientDICOM": [0.996278, 0.0842897, 0.018012, -0.0745609, 0.947641, -0.310512], "ImageOrientationText": "Tra>Cor(-18.0)>Sag(2.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,19 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-01_ses-011_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-011/func/sub-01_ses-011_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-011/func/sub-01_ses-011_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-011/func/sub-01_ses-011_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-011/func/sub-01_ses-011_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +67,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 622, - -7196, - -8826, - 661, - 122, - 44, - -47, - 13 - ], + "ShimSetting": [622, -7196, -8826, 661, 122, 44, -47, 13], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_epi.json index 8076ad23b..00a42160d 100644 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996278, - 0.0842897, - 0.018012, - -0.0745609, - 0.947641, - -0.310512 - ], + "ImageOrientationPatientDICOM": [0.996278, 0.0842897, 0.018012, -0.0745609, 0.947641, -0.310512], "ImageOrientationText": "Tra>Cor(-18.0)>Sag(2.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-01_ses-011_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 622, - -7196, - -8826, - 661, - 122, - 44, - -47, - 13 - ], + "ShimSetting": [622, -7196, -8826, 661, 122, 44, -47, 13], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_epi.json index ba27e9fb7..985153bbc 100644 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996278, - 0.0842897, - 0.018012, - -0.0745609, - 0.947641, - -0.310512 - ], + "ImageOrientationPatientDICOM": [0.996278, 0.0842897, 0.018012, -0.0745609, 0.947641, -0.310512], "ImageOrientationText": "Tra>Cor(-18.0)>Sag(2.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-01_ses-011_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 622, - -7196, - -8826, - 661, - 122, - 44, - -47, - 13 - ], + "ShimSetting": [622, -7196, -8826, 661, 122, 44, -47, 13], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_epi.json index 952c9ac53..d431c626e 100644 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996278, - 0.0842897, - 0.018012, - -0.0745609, - 0.947641, - -0.310512 - ], + "ImageOrientationPatientDICOM": [0.996278, 0.0842897, 0.018012, -0.0745609, 0.947641, -0.310512], "ImageOrientationText": "Tra>Cor(-18.0)>Sag(2.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-01_ses-011_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 622, - -7196, - -8826, - 661, - 122, - 44, - -47, - 13 - ], + "ShimSetting": [622, -7196, -8826, 661, 122, 44, -47, 13], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_epi.json index f5fc83ac0..9b8a20e97 100644 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996278, - 0.0842897, - 0.018012, - -0.0745609, - 0.947641, - -0.310512 - ], + "ImageOrientationPatientDICOM": [0.996278, 0.0842897, 0.018012, -0.0745609, 0.947641, -0.310512], "ImageOrientationText": "Tra>Cor(-18.0)>Sag(2.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-01_ses-011_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 622, - -7196, - -8826, - 661, - 122, - 44, - -47, - 13 - ], + "ShimSetting": [622, -7196, -8826, 661, 122, 44, -47, 13], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_epi.json b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_epi.json index b39427330..1f2f0cbc6 100644 --- a/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-01/ses-011/fmap/sub-01_ses-011_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996278, - 0.0842897, - 0.018012, - -0.0745609, - 0.947641, - -0.310512 - ], + "ImageOrientationPatientDICOM": [0.996278, 0.0842897, 0.018012, -0.0745609, 0.947641, -0.310512], "ImageOrientationText": "Tra>Cor(-18.0)>Sag(2.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-01_ses-011_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 622, - -7196, - -8826, - 661, - 122, - 44, - -47, - 13 - ], + "ShimSetting": [622, -7196, -8826, 661, 122, 44, -47, 13], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From bcbfb9fd82223a1c7cfef2204c7807579bcaef18 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:42:01 -0400 Subject: [PATCH 134/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-014_acq-axial_localizer.json | 81 +++ .../sub-02_ses-014_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-014_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-014_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-014_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-014_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-014/anat/sub-02_ses-014_scout.json | 542 ++++++++++++++++++ .../ses-014/anat/sub-02_ses-014_scout.nii.gz | 1 + ...4_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-014_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...14_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...014_task-mario3_run-01_part-mag_events.tsv | 1 + ...014_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...14_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-01_part-phase_events.tsv | 1 + ...4_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-014_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...14_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...014_task-mario3_run-02_part-mag_events.tsv | 1 + ...014_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...14_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-02_part-phase_events.tsv | 1 + ...4_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-014_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...14_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...014_task-mario3_run-03_part-mag_events.tsv | 1 + ...014_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...14_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-03_part-phase_events.tsv | 1 + ...4_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-014_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...14_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...014_task-mario3_run-04_part-mag_events.tsv | 1 + ...014_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...14_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-04_part-phase_events.tsv | 1 + ...4_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-02/ses-014/sub-02_ses-014_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5409 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-014/anat/sub-02_ses-014_acq-axial_localizer.json create mode 120000 sub-02/ses-014/anat/sub-02_ses-014_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-014/anat/sub-02_ses-014_acq-coronal_localizer.json create mode 120000 sub-02/ses-014/anat/sub-02_ses-014_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-014/anat/sub-02_ses-014_acq-sagittal_localizer.json create mode 120000 sub-02/ses-014/anat/sub-02_ses-014_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-014/anat/sub-02_ses-014_scout.json create mode 120000 sub-02/ses-014/anat/sub-02_ses-014_scout.nii.gz create mode 100644 sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_part-phase_sbref.nii.gz create mode 120000 sub-02/ses-014/sub-02_ses-014_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index fecbe2dd7..660f267c6 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit fecbe2dd7c7d1d10db2a9f1a8717fb47e015f042 +Subproject commit 660f267c697b86795670898a3953145454b64021 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..83ada7a9d --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 51 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-014/anat/sub-02_ses-014_acq-axial_localizer.json b/sub-02/ses-014/anat/sub-02_ses-014_acq-axial_localizer.json new file mode 100644 index 000000000..b702c4c0d --- /dev/null +++ b/sub-02/ses-014/anat/sub-02_ses-014_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:14:56.020000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0332909, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 261.813 +} \ No newline at end of file diff --git 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"TxRefAmp": 261.813, + "dcmmeta_affine": [ + [-1.9966078996658325, 0.03031959757208824, 0.11241777241230011, 101.96884155273438], + [-0.036207761615514755, 1.6735827922821045, -1.0944448709487915, -44.98036575317383], + [0.11066178977489471, 1.0946238040924072, 1.6701953411102295, -101.68331146240234], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From c7ef99d1b35f09646f5845b5402b9cc081cf461c Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:42:33 -0400 Subject: [PATCH 135/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-025_acq-axial_localizer.json | 81 +++ .../sub-01_ses-025_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-025_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-025_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-025_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-025_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-025/anat/sub-01_ses-025_scout.json | 542 ++++++++++++++++++ .../ses-025/anat/sub-01_ses-025_scout.nii.gz | 1 + ...5_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-025_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...25_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...025_task-mario3_run-01_part-mag_events.tsv | 1 + ...025_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...25_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-01_part-phase_events.tsv | 1 + ...5_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-025_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...25_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...025_task-mario3_run-02_part-mag_events.tsv | 1 + ...025_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...25_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-02_part-phase_events.tsv | 1 + ...5_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-025_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...25_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...k-mario3_run-03_part-mag_bold__dup-01.json | 172 ++++++ ...mario3_run-03_part-mag_bold__dup-01.nii.gz | 1 + ...025_task-mario3_run-03_part-mag_events.tsv | 1 + ...025_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...25_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...mario3_run-03_part-phase_bold__dup-01.json | 178 ++++++ ...rio3_run-03_part-phase_bold__dup-01.nii.gz | 1 + ...5_task-mario3_run-03_part-phase_events.tsv | 1 + ...5_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-mario3_run-03_sbref__part-mag_dup-01.json | 150 +++++ ...ario3_run-03_sbref__part-mag_dup-01.nii.gz | 1 + ...ario3_run-03_sbref__part-phase_dup-01.json | 153 +++++ ...io3_run-03_sbref__part-phase_dup-01.nii.gz | 1 + sub-01/ses-025/sub-01_ses-025_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 77 files changed, 5407 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-025/anat/sub-01_ses-025_acq-axial_localizer.json create mode 120000 sub-01/ses-025/anat/sub-01_ses-025_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-025/anat/sub-01_ses-025_acq-coronal_localizer.json create mode 120000 sub-01/ses-025/anat/sub-01_ses-025_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-025/anat/sub-01_ses-025_acq-sagittal_localizer.json create mode 120000 sub-01/ses-025/anat/sub-01_ses-025_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-025/anat/sub-01_ses-025_scout.json create mode 120000 sub-01/ses-025/anat/sub-01_ses-025_scout.nii.gz create mode 100644 sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-mag_bold.nii.gz create mode 100644 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-mag_bold__dup-01.json create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-mag_bold__dup-01.nii.gz create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-phase_bold.nii.gz create mode 100644 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-phase_bold__dup-01.json create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-phase_bold__dup-01.nii.gz create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_sbref__part-mag_dup-01.json create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_sbref__part-mag_dup-01.nii.gz create mode 100644 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_sbref__part-phase_dup-01.json create mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_sbref__part-phase_dup-01.nii.gz create mode 120000 sub-01/ses-025/sub-01_ses-025_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index b90c06fee..5c04abadf 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit b90c06fee70f2b7f20ce48f1f9612f19456d5a55 +Subproject commit 5c04abadf706e012bd69a24b4a646aca3764e433 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..4708c7800 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 46 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-025/anat/sub-01_ses-025_acq-axial_localizer.json b/sub-01/ses-025/anat/sub-01_ses-025_acq-axial_localizer.json new file mode 100644 index 000000000..a341c19cd --- /dev/null +++ b/sub-01/ses-025/anat/sub-01_ses-025_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:40:57.070000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0299314, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 599, + -7229, + -9119, + -10, + 50, + -38, + -82, + 55 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 241.933 +} \ No newline at end of file diff --git a/sub-01/ses-025/anat/sub-01_ses-025_acq-axial_localizer.nii.gz b/sub-01/ses-025/anat/sub-01_ses-025_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..0e76c142a --- /dev/null +++ b/sub-01/ses-025/anat/sub-01_ses-025_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/4P/F8/MD5E-s184056--002316bf7d870352ca410a42982ee885.nii.gz/MD5E-s184056--002316bf7d870352ca410a42982ee885.nii.gz \ No newline at end of file diff --git a/sub-01/ses-025/anat/sub-01_ses-025_acq-coronal_localizer.json b/sub-01/ses-025/anat/sub-01_ses-025_acq-coronal_localizer.json new file mode 100644 index 000000000..fac0ca655 --- /dev/null +++ b/sub-01/ses-025/anat/sub-01_ses-025_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:41:4.060000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": 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r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_sbref__part-mag_dup-01.nii.gz b/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_sbref__part-mag_dup-01.nii.gz new file mode 120000 index 000000000..1c4785887 --- /dev/null +++ b/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_sbref__part-mag_dup-01.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/p7/Q6/MD5E-s1114549--7b78170671126dd04238fca38608ebe9.nii.gz/MD5E-s1114549--7b78170671126dd04238fca38608ebe9.nii.gz \ No newline at end of file diff --git a/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_sbref__part-phase_dup-01.json b/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_sbref__part-phase_dup-01.json new file mode 100644 index 000000000..3edece60f --- /dev/null +++ b/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_sbref__part-phase_dup-01.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + 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+../../.git/annex/objects/mQ/QP/MD5E-s3321--356285dfe378d9cdae89b06f26182a2c.tsv/MD5E-s3321--356285dfe378d9cdae89b06f26182a2c.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..cc2310fcc --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": 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No newline at end of file From 3f9a7a78a4d5f2762f54787e63c40c64989fa195 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:42:34 -0400 Subject: [PATCH 136/463] fix fmap phase --- ...2_ses-014_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-014_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-014_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-014_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-014_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-014_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-014_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-02/ses-014/sub-02_ses-014_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-02/ses-014/fmap/{sub-02_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-014_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-014/fmap/{sub-02_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-014_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-014/fmap/{sub-02_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-014_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-014/fmap/{sub-02_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-014_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-014/fmap/{sub-02_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-014_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-014/fmap/{sub-02_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-014_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-014/fmap/{sub-02_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-014_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-014/fmap/{sub-02_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-014_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-014/fmap/{sub-02_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-014_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-014/fmap/{sub-02_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-014_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-02/ses-014/fmap/{sub-02_ses-014_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-02_ses-014_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-02/ses-014/fmap/{sub-02_ses-014_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-02_ses-014_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 893b77a75..000000000 --- a/sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:15:59.095000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": 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0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99830393243773, 0.01810388142486, 0.05533089513759, 0.01515979848011, 0.83679139524025, -0.5473119232777], - "ImagePositionPatient": [-842.89335280159, -749.76242172956, 369.22513466305], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.26031, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "161411.318000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.0391049979186, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "161645.570000", - "SliceLocation": -54.569675612204, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.999999987092, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "161411.236000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["161559.095000", "161600.585000", "161602.075000"], - "ContentTime": ["161645.572000", "161645.582000", "161645.585000"], - "InstanceCreationTime": ["161645.572000", "161645.582000", "161645.585000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4732.0, 4734.0, 4736.0], - "WindowWidth": [18550.0, 18546.0, 18552.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index d88abcd62..000000000 --- a/sub-02/ses-014/fmap/sub-02_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/gW/3K/MD5E-s3332966--c0bc127d9d6e4a0a1124bfdfa8d20064.nii.gz/MD5E-s3332966--c0bc127d9d6e4a0a1124bfdfa8d20064.nii.gz \ No newline at end of file diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 262812768..000000000 --- a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:15:48.665000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998304, - 0.0181039, - 0.0553309, - 0.0151598, - 0.836791, - -0.547312 - ], - "ImageOrientationText": "Tra>Cor(-33.2)>Sag(3.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.039105, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 616, - -7188, - -8874, - 253, - 13, - -235, - -26, - 51 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 261.813, - "WipMemBlock": "572d7991-0ae4-4046-88fa-61b03ad702df||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 68b4aa6ee..000000000 --- a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/1j/Fk/MD5E-s1112127--a371e00741f1a5ed8cd54a94e41ce021.nii.gz/MD5E-s1112127--a371e00741f1a5ed8cd54a94e41ce021.nii.gz \ No newline at end of file diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 7d315cf43..000000000 --- a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:17:11.222500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998304, - 0.0181039, - 0.0553309, - 0.0151598, - 0.836791, - -0.547312 - ], - "ImageOrientationText": "Tra>Cor(-33.2)>Sag(3.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0490342, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 616, - -7188, - -8874, - 253, - 13, - -235, - -26, - 51 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 261.813, - "WipMemBlock": "14685f3e-eb33-4847-bc6e-5c87dc053d44||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 8d87a0658..000000000 --- a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/V8/gm/MD5E-s1103626--56d2f53bd4f801aa2c0a1eac2c08e611.nii.gz/MD5E-s1103626--56d2f53bd4f801aa2c0a1eac2c08e611.nii.gz \ No newline at end of file diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index e429f9e56..000000000 --- a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:28:22.495000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998304, - 0.0181039, - 0.0553309, - 0.0151598, - 0.836791, - -0.547312 - ], - "ImageOrientationText": "Tra>Cor(-33.2)>Sag(3.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0490342, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 616, - -7188, - -8874, - 253, - 13, - -235, - -26, - 51 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 261.813, - "WipMemBlock": "f70a8710-5c7b-46c1-8884-371a028777ce||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 8049a773a..000000000 --- a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/44/3z/MD5E-s1103422--1d26709e934cd44ba7114ba6a3b7be4a.nii.gz/MD5E-s1103422--1d26709e934cd44ba7114ba6a3b7be4a.nii.gz \ No newline at end of file diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 40b7576e5..000000000 --- a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:38:12.025000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998304, - 0.0181039, - 0.0553309, - 0.0151598, - 0.836791, - -0.547312 - ], - "ImageOrientationText": "Tra>Cor(-33.2)>Sag(3.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0490342, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 616, - -7188, - -8874, - 253, - 13, - -235, - -26, - 51 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 261.813, - "WipMemBlock": "23a72194-4067-4d53-a5dc-1a837ee53d68||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 35442a6c0..000000000 --- a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Z7/3K/MD5E-s1103530--0b8f87a1b2130af9fbc96e8bec601940.nii.gz/MD5E-s1103530--0b8f87a1b2130af9fbc96e8bec601940.nii.gz \ No newline at end of file diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 9c56fbf20..000000000 --- a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:48:3.057500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998304, - 0.0181039, - 0.0553309, - 0.0151598, - 0.836791, - -0.547312 - ], - "ImageOrientationText": "Tra>Cor(-33.2)>Sag(3.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0490342, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 616, - -7188, - -8874, - 253, - 13, - -235, - -26, - 51 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 261.813, - "WipMemBlock": "647e3157-2266-481c-b005-93b8f0ab266e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index a082b00ad..000000000 --- a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/jQ/zV/MD5E-s1103566--07eb2124e74f6c1bf83485af53fd5c59.nii.gz/MD5E-s1103566--07eb2124e74f6c1bf83485af53fd5c59.nii.gz \ No newline at end of file diff --git a/sub-02/ses-014/sub-02_ses-014_scans.tsv b/sub-02/ses-014/sub-02_ses-014_scans.tsv index acbb86139..fba4122f2 120000 --- a/sub-02/ses-014/sub-02_ses-014_scans.tsv +++ b/sub-02/ses-014/sub-02_ses-014_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/4j/jK/MD5E-s3289--ef6a1afde411ca251e4983811be07a7a.tsv/MD5E-s3289--ef6a1afde411ca251e4983811be07a7a.tsv \ No newline at end of file +../../.git/annex/objects/JQ/w7/MD5E-s2567--df86e86c4c577226092e4e169106e017.tsv/MD5E-s2567--df86e86c4c577226092e4e169106e017.tsv \ No newline at end of file From 61a516a988a31d9cb2cf1916dd7f0d3bade1ef98 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:42:43 -0400 Subject: [PATCH 137/463] fix complex event files --- ...g_events.tsv => sub-02_ses-014_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-02_ses-014_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-02_ses-014_task-mario3_run-03_events.tsv} | 0 .../func/sub-02_ses-014_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-02_ses-014_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-02_ses-014_task-mario3_run-04_events.tsv} | 0 .../func/sub-02_ses-014_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-02_ses-014_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-02/ses-014/func/{sub-02_ses-014_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-014_task-mario3_run-01_events.tsv} (100%) rename sub-02/ses-014/func/{sub-02_ses-014_task-mario3_run-01_part-phase_events.tsv => sub-02_ses-014_task-mario3_run-02_events.tsv} (100%) rename sub-02/ses-014/func/{sub-02_ses-014_task-mario3_run-02_part-mag_events.tsv => sub-02_ses-014_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_part-phase_events.tsv rename sub-02/ses-014/func/{sub-02_ses-014_task-mario3_run-02_part-phase_events.tsv => sub-02_ses-014_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-02_events.tsv similarity index 100% rename from sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-01_part-phase_events.tsv rename to sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-02_events.tsv diff --git a/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-02_part-mag_events.tsv b/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_events.tsv similarity index 100% rename from sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-02_part-mag_events.tsv rename to sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_events.tsv diff --git a/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_part-mag_events.tsv b/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-02_part-phase_events.tsv b/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_events.tsv similarity index 100% rename from sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-02_part-phase_events.tsv rename to sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_events.tsv diff --git a/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_part-mag_events.tsv b/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_part-phase_events.tsv b/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-014/func/sub-02_ses-014_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 1c8821ce91f9be658b44525228b6e6028047972a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:43:10 -0400 Subject: [PATCH 138/463] fix fmap phase --- ...1_ses-025_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-025_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-025_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-025_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-025_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-025_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-025_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-025_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-025_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-025_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-025_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-025_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-01/ses-025/sub-01_ses-025_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-01/ses-025/fmap/{sub-01_ses-025_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-025_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-025/fmap/{sub-01_ses-025_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-025_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-025/fmap/{sub-01_ses-025_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-025_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-025/fmap/{sub-01_ses-025_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-025_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-025/fmap/{sub-01_ses-025_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-025_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-025/fmap/{sub-01_ses-025_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-025_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-025/fmap/{sub-01_ses-025_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-025_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-025/fmap/{sub-01_ses-025_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-025_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-01/ses-025/fmap/{sub-01_ses-025_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-01_ses-025_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-01/ses-025/fmap/{sub-01_ses-025_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-01_ses-025_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-01/ses-025/fmap/{sub-01_ses-025_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-01_ses-025_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-01/ses-025/fmap/{sub-01_ses-025_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-01_ses-025_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index c006ed39d..000000000 --- a/sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:42:16.115000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.993707, 0.105658, 0.0371847, -0.0839679, 0.922394, -0.377014], - "ImageOrientationText": "Tra>Cor(-21.9)>Sag(4.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0351588, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [623, -7233, -8805, 589, 178, -29, -117, 89], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 241.933, - "WipMemBlock": "2e9a2dbe-5f92-4089-8999-8bd796441343||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.987414002418518, -0.16793577373027802, 0.1482672095298767, 109.53636932373047], - [-0.2113168090581894, 1.8447870016098022, -0.7430384159088135, -54.176029205322266], - [0.07436934113502502, 0.7540281414985657, 1.850921630859375, -64.9248275756836], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99370700021513, 0.10565840303667, 0.03718466876526, -0.083967890426, 0.92239350207616, -0.3770140855526], - "ImagePositionPatient": [-754.52905657398, -884.25881891923, 260.13588856407], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.259022, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "113932.884000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.03515875450673, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "114302.719000", - "SliceLocation": -31.837621406655, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000119433, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "113932.765000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["114216.115000", "114217.605000", "114219.095000"], - "ContentTime": ["114302.721000", "114302.723000", "114302.726000"], - "InstanceCreationTime": ["114302.721000", "114302.723000", "114302.726000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4772.0, 4772.0, 4798.0], - "WindowWidth": [18580.0, 18582.0, 18614.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index ac02335ef..000000000 --- a/sub-01/ses-025/fmap/sub-01_ses-025_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/KF/WX/MD5E-s3335271--38e032f4c9c11458f9a66cfd41aa0764.nii.gz/MD5E-s3335271--38e032f4c9c11458f9a66cfd41aa0764.nii.gz \ No newline at end of file diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 25f1cb7ca..000000000 --- a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:42:5.685000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993707, - 0.105658, - 0.0371847, - -0.0839679, - 0.922394, - -0.377014 - ], - "ImageOrientationText": "Tra>Cor(-21.9)>Sag(4.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0351588, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 623, - -7233, - -8805, - 589, - 178, - -29, - -117, - 89 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 241.933, - "WipMemBlock": "2e9a2dbe-5f92-4089-8999-8bd796441343||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 12a2d1854..000000000 --- a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/xp/zx/MD5E-s1112418--1c9a3467c9083cff1da0a96f64e3f09f.nii.gz/MD5E-s1112418--1c9a3467c9083cff1da0a96f64e3f09f.nii.gz \ No newline at end of file diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index c0295784e..000000000 --- a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:43:58.220000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993707, - 0.105658, - 0.0371847, - -0.0839679, - 0.922394, - -0.377014 - ], - "ImageOrientationText": "Tra>Cor(-21.9)>Sag(4.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.044086, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 623, - -7233, - -8805, - 589, - 178, - -29, - -117, - 89 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 241.933, - "WipMemBlock": "08cb4485-97eb-4449-8506-e540ab79f5c2||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 84fbe2521..000000000 --- a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Pq/8X/MD5E-s1104032--55670d839e0fb0284f11999293891865.nii.gz/MD5E-s1104032--55670d839e0fb0284f11999293891865.nii.gz \ No newline at end of file diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 4e42683a1..000000000 --- a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:54:34.427500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993707, - 0.105658, - 0.0371847, - -0.0839679, - 0.922394, - -0.377014 - ], - "ImageOrientationText": "Tra>Cor(-21.9)>Sag(4.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.044086, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 623, - -7233, - -8805, - 589, - 178, - -29, - -117, - 89 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 241.933, - "WipMemBlock": "6272fd3a-489d-420c-b09a-6a4198fc7199||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 0b905512b..000000000 --- a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/jM/q9/MD5E-s1103849--2125bbd013d139460c88aa6b178dc513.nii.gz/MD5E-s1103849--2125bbd013d139460c88aa6b178dc513.nii.gz \ No newline at end of file diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index e3657288b..000000000 --- a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "12:05:34.165000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993707, - 0.105658, - 0.0371847, - -0.0839679, - 0.922394, - -0.377014 - ], - "ImageOrientationText": "Tra>Cor(-21.9)>Sag(4.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.044086, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 623, - -7233, - -8805, - 589, - 178, - -29, - -117, - 89 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 241.933, - "WipMemBlock": "48df2a1d-df5c-4c86-a068-cdb4c9edf424||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index bdfcd7c1d..000000000 --- a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/F2/2x/MD5E-s1103862--4b8381e2172948d214a74ee7b902b537.nii.gz/MD5E-s1103862--4b8381e2172948d214a74ee7b902b537.nii.gz \ No newline at end of file diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 2438a46fb..000000000 --- a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "12:11:17.752500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993707, - 0.105658, - 0.0371847, - -0.0839679, - 0.922394, - -0.377014 - ], - "ImageOrientationText": "Tra>Cor(-21.9)>Sag(4.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.044086, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 623, - -7233, - -8805, - 589, - 178, - -29, - -117, - 89 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 241.933, - "WipMemBlock": "0398e1c7-9a8e-405f-a699-79b2041673c5||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 04081bec7..000000000 --- a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3K/vF/MD5E-s1103798--c272e70bf4817d2958ba78969a0c93e5.nii.gz/MD5E-s1103798--c272e70bf4817d2958ba78969a0c93e5.nii.gz \ No newline at end of file diff --git a/sub-01/ses-025/sub-01_ses-025_scans.tsv b/sub-01/ses-025/sub-01_ses-025_scans.tsv index 59c10fdd6..4e31759a1 120000 --- a/sub-01/ses-025/sub-01_ses-025_scans.tsv +++ b/sub-01/ses-025/sub-01_ses-025_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/mQ/QP/MD5E-s3321--356285dfe378d9cdae89b06f26182a2c.tsv/MD5E-s3321--356285dfe378d9cdae89b06f26182a2c.tsv \ No newline at end of file +../../.git/annex/objects/Xk/p4/MD5E-s2599--5e7a6d461aa92882b654d5b57d86ecd0.tsv/MD5E-s2599--5e7a6d461aa92882b654d5b57d86ecd0.tsv \ No newline at end of file From bcf1c945b2ac2caee16651e95d8f2a693b13518a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:43:16 -0400 Subject: [PATCH 139/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..f75db930b --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 2f7689ce-d885-4750-a85f-649e86cc7996 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..4448aaa0f --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 4448aaa0f64803de4931776018efcc64f33f6d9c From 2bad083961be54ac564f121e5109386d9918ec8c Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:43:18 -0400 Subject: [PATCH 140/463] fix complex event files --- ...g_events.tsv => sub-01_ses-025_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-025_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-025_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-01_ses-025_task-mario3_run-03_events.tsv} | 0 .../func/sub-01_ses-025_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-01_ses-025_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-01/ses-025/func/{sub-01_ses-025_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-025_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-025/func/{sub-01_ses-025_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-025_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_part-phase_events.tsv rename sub-01/ses-025/func/{sub-01_ses-025_task-mario3_run-02_part-mag_events.tsv => sub-01_ses-025_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_events.tsv similarity index 100% rename from sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_part-mag_events.tsv rename to sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_events.tsv diff --git a/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-mag_events.tsv b/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 6f29b82cd2a23316b86b4a62881d5671bcd633cf Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:43:28 -0400 Subject: [PATCH 141/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..745510ffa --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 04e350b8-a6b0-4473-93ed-6a5de65bf86e diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..f414bbddf --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit f414bbddf5d455ee433f54c37dedb362c39025c4 From 0a7a22b65c50e4a36c0436d0d93c0d12b00c7f35 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:43:38 -0400 Subject: [PATCH 142/463] fill IntendedFor --- ...2_ses-014_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...2_ses-014_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...2_ses-014_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...2_ses-014_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...2_ses-014_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_epi.json index e9baa36de..2f1db77bf 100644 --- a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998304, - 0.0181039, - 0.0553309, - 0.0151598, - 0.836791, - -0.547312 - ], + "ImageOrientationPatientDICOM": [0.998304, 0.0181039, 0.0553309, 0.0151598, 0.836791, -0.547312], "ImageOrientationText": "Tra>Cor(-33.2)>Sag(3.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-02_ses-014_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-014/func/sub-02_ses-014_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-014/func/sub-02_ses-014_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-014/func/sub-02_ses-014_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 616, - -7188, - -8874, - 253, - 13, - -235, - -26, - 51 - ], + "ShimSetting": [616, -7188, -8874, 253, 13, -235, -26, 51], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_epi.json b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_epi.json index 3f92021af..e50c9ddbe 100644 --- a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998304, - 0.0181039, - 0.0553309, - 0.0151598, - 0.836791, - -0.547312 - ], + "ImageOrientationPatientDICOM": [0.998304, 0.0181039, 0.0553309, 0.0151598, 0.836791, -0.547312], "ImageOrientationText": "Tra>Cor(-33.2)>Sag(3.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-02_ses-014_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 616, - -7188, - -8874, - 253, - 13, - -235, - -26, - 51 - ], + "ShimSetting": [616, -7188, -8874, 253, 13, -235, -26, 51], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_epi.json b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_epi.json index 0219cbc04..f28f6e7fc 100644 --- a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998304, - 0.0181039, - 0.0553309, - 0.0151598, - 0.836791, - -0.547312 - ], + "ImageOrientationPatientDICOM": [0.998304, 0.0181039, 0.0553309, 0.0151598, 0.836791, -0.547312], "ImageOrientationText": "Tra>Cor(-33.2)>Sag(3.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-02_ses-014_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 616, - -7188, - -8874, - 253, - 13, - -235, - -26, - 51 - ], + "ShimSetting": [616, -7188, -8874, 253, 13, -235, -26, 51], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_epi.json b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_epi.json index 27818cb26..bc199a22a 100644 --- a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998304, - 0.0181039, - 0.0553309, - 0.0151598, - 0.836791, - -0.547312 - ], + "ImageOrientationPatientDICOM": [0.998304, 0.0181039, 0.0553309, 0.0151598, 0.836791, -0.547312], "ImageOrientationText": "Tra>Cor(-33.2)>Sag(3.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-02_ses-014_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 616, - -7188, - -8874, - 253, - 13, - -235, - -26, - 51 - ], + "ShimSetting": [616, -7188, -8874, 253, 13, -235, -26, 51], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_epi.json b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_epi.json index c728f9a30..f4d8c7e4f 100644 --- a/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-02/ses-014/fmap/sub-02_ses-014_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998304, - 0.0181039, - 0.0553309, - 0.0151598, - 0.836791, - -0.547312 - ], + "ImageOrientationPatientDICOM": [0.998304, 0.0181039, 0.0553309, 0.0151598, 0.836791, -0.547312], "ImageOrientationText": "Tra>Cor(-33.2)>Sag(3.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-02_ses-014_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 616, - -7188, - -8874, - 253, - 13, - -235, - -26, - 51 - ], + "ShimSetting": [616, -7188, -8874, 253, 13, -235, -26, 51], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From c238befeafcd293e75e77cf930670e80c5d4e66d Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:43:45 -0400 Subject: [PATCH 143/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-015_acq-axial_localizer.json | 81 +++ .../sub-02_ses-015_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-015_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-015_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-015_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-015_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-015/anat/sub-02_ses-015_scout.json | 542 ++++++++++++++++++ .../ses-015/anat/sub-02_ses-015_scout.nii.gz | 1 + ...5_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-015_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...15_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...015_task-mario3_run-01_part-mag_events.tsv | 1 + ...015_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...15_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-01_part-phase_events.tsv | 1 + ...5_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-015_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...15_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...015_task-mario3_run-02_part-mag_events.tsv | 1 + ...015_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...15_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-02_part-phase_events.tsv | 1 + ...5_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-015_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...15_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...015_task-mario3_run-03_part-mag_events.tsv | 1 + ...015_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...15_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-03_part-phase_events.tsv | 1 + ...5_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-015_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...15_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...015_task-mario3_run-04_part-mag_events.tsv | 1 + ...015_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...15_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-04_part-phase_events.tsv | 1 + ...5_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-02/ses-015/sub-02_ses-015_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5409 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-015/anat/sub-02_ses-015_acq-axial_localizer.json create mode 120000 sub-02/ses-015/anat/sub-02_ses-015_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-015/anat/sub-02_ses-015_acq-coronal_localizer.json create mode 120000 sub-02/ses-015/anat/sub-02_ses-015_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-015/anat/sub-02_ses-015_acq-sagittal_localizer.json create mode 120000 sub-02/ses-015/anat/sub-02_ses-015_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-015/anat/sub-02_ses-015_scout.json create mode 120000 sub-02/ses-015/anat/sub-02_ses-015_scout.nii.gz create mode 100644 sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_part-phase_sbref.nii.gz create mode 120000 sub-02/ses-015/sub-02_ses-015_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 4448aaa0f..deacf15d9 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 4448aaa0f64803de4931776018efcc64f33f6d9c +Subproject commit deacf15d9a030dfbfc94c17a4142d033c7a661a1 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..83ada7a9d --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 51 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-015/anat/sub-02_ses-015_acq-axial_localizer.json b/sub-02/ses-015/anat/sub-02_ses-015_acq-axial_localizer.json new file mode 100644 index 000000000..ec37c995d --- /dev/null +++ b/sub-02/ses-015/anat/sub-02_ses-015_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:09:14.045000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0479642, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 308.032 +} \ No newline at end of file diff --git a/sub-02/ses-015/anat/sub-02_ses-015_acq-axial_localizer.nii.gz b/sub-02/ses-015/anat/sub-02_ses-015_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..b357b9940 --- /dev/null +++ b/sub-02/ses-015/anat/sub-02_ses-015_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Fk/jJ/MD5E-s188741--5827dcdc23695797b26870761a3dbddd.nii.gz/MD5E-s188741--5827dcdc23695797b26870761a3dbddd.nii.gz \ No newline at end of file diff --git a/sub-02/ses-015/anat/sub-02_ses-015_acq-coronal_localizer.json b/sub-02/ses-015/anat/sub-02_ses-015_acq-coronal_localizer.json new file mode 100644 index 000000000..742fb5b81 --- /dev/null +++ b/sub-02/ses-015/anat/sub-02_ses-015_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:09:21.035000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0479642, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 308.032 +} \ No newline at end of file diff --git a/sub-02/ses-015/anat/sub-02_ses-015_acq-coronal_localizer.nii.gz b/sub-02/ses-015/anat/sub-02_ses-015_acq-coronal_localizer.nii.gz new file mode 120000 index 000000000..3b16de11e --- /dev/null +++ b/sub-02/ses-015/anat/sub-02_ses-015_acq-coronal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/gx/4K/MD5E-s203355--faede67d1532981b4f2400db9d8c7cbf.nii.gz/MD5E-s203355--faede67d1532981b4f2400db9d8c7cbf.nii.gz \ No newline at end of file diff --git a/sub-02/ses-015/anat/sub-02_ses-015_acq-sagittal_localizer.json b/sub-02/ses-015/anat/sub-02_ses-015_acq-sagittal_localizer.json new file mode 100644 index 000000000..1ec7d8a57 --- /dev/null +++ b/sub-02/ses-015/anat/sub-02_ses-015_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:09:7.055000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": 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"IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0706465, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [614, -7191, -8860, 215, 49, -213, -28, 49], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 308.032, + "dcmmeta_affine": [ + [-1.9986993074417114, 0.030351394787430763, 0.06542108952999115, 104.5475082397461], + [-0.00982957985252142, 1.6826802492141724, -1.0809675455093384, -47.32787322998047], + [0.07144582271575928, 1.0805859565734863, 1.6814367771148682, -87.17710876464844], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 35ee32a54754d56d01f82cd2c43dfa9168a58898 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:43:56 -0400 Subject: [PATCH 144/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-013_acq-axial_localizer.json | 81 +++ .../sub-01_ses-013_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-013_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-013_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-013_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-013_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-013/anat/sub-01_ses-013_scout.json | 542 ++++++++++++++++++ .../ses-013/anat/sub-01_ses-013_scout.nii.gz | 1 + ...3_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ...-013_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...13_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...013_task-mario3_run-01_part-mag_events.tsv | 1 + ...013_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...13_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-01_part-phase_events.tsv | 1 + ...3_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-013_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...13_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...013_task-mario3_run-02_part-mag_events.tsv | 1 + ...013_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...13_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-02_part-phase_events.tsv | 1 + ...3_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + sub-01/ses-013/sub-01_ses-013_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 51 files changed, 3485 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-013/anat/sub-01_ses-013_acq-axial_localizer.json create mode 120000 sub-01/ses-013/anat/sub-01_ses-013_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-013/anat/sub-01_ses-013_acq-coronal_localizer.json create mode 120000 sub-01/ses-013/anat/sub-01_ses-013_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-013/anat/sub-01_ses-013_acq-sagittal_localizer.json create mode 120000 sub-01/ses-013/anat/sub-01_ses-013_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-013/anat/sub-01_ses-013_scout.json create mode 120000 sub-01/ses-013/anat/sub-01_ses-013_scout.nii.gz create mode 100644 sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-phase_sbref.nii.gz create mode 120000 sub-01/ses-013/sub-01_ses-013_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index f414bbddf..ea49a7fbd 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit f414bbddf5d455ee433f54c37dedb362c39025c4 +Subproject commit ea49a7fbdb5f09957335a3b90326d3fb18d1e683 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-013/anat/sub-01_ses-013_acq-axial_localizer.json b/sub-01/ses-013/anat/sub-01_ses-013_acq-axial_localizer.json new file mode 100644 index 000000000..cfb7a5b02 --- /dev/null +++ b/sub-01/ses-013/anat/sub-01_ses-013_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:34:53.022500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0395719, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 274.534 +} \ No newline at end of file diff --git a/sub-01/ses-013/anat/sub-01_ses-013_acq-axial_localizer.nii.gz b/sub-01/ses-013/anat/sub-01_ses-013_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..280eb0d0f --- /dev/null +++ b/sub-01/ses-013/anat/sub-01_ses-013_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/6J/XK/MD5E-s184999--e27988315230208b3ebd9fc54cd43815.nii.gz/MD5E-s184999--e27988315230208b3ebd9fc54cd43815.nii.gz \ No newline at end of file diff --git a/sub-01/ses-013/anat/sub-01_ses-013_acq-coronal_localizer.json b/sub-01/ses-013/anat/sub-01_ses-013_acq-coronal_localizer.json new file mode 100644 index 000000000..eaf8e1621 --- /dev/null +++ b/sub-01/ses-013/anat/sub-01_ses-013_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:35:0.012500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0395719, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 274.534 +} \ No newline at end of file diff --git a/sub-01/ses-013/anat/sub-01_ses-013_acq-coronal_localizer.nii.gz b/sub-01/ses-013/anat/sub-01_ses-013_acq-coronal_localizer.nii.gz new file mode 120000 index 000000000..3c5215316 --- /dev/null +++ b/sub-01/ses-013/anat/sub-01_ses-013_acq-coronal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Jw/6Q/MD5E-s199659--232a0d0b2cc6cd317174e1fbb1d49085.nii.gz/MD5E-s199659--232a0d0b2cc6cd317174e1fbb1d49085.nii.gz \ No newline at end of file diff --git a/sub-01/ses-013/anat/sub-01_ses-013_acq-sagittal_localizer.json b/sub-01/ses-013/anat/sub-01_ses-013_acq-sagittal_localizer.json new file mode 100644 index 000000000..1657a1396 --- /dev/null +++ b/sub-01/ses-013/anat/sub-01_ses-013_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:34:46.032500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 0, + 1, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Sag", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + 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b/sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-phase_events.tsv new file mode 120000 index 000000000..1bbdfddb5 --- /dev/null +++ b/sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-phase_events.tsv @@ -0,0 +1 @@ +../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-phase_sbref.json b/sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-phase_sbref.json new file mode 100644 index 000000000..4e96a73f3 --- /dev/null +++ b/sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-phase_sbref.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:47:55.747500", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": 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b/sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-phase_sbref.nii.gz new file mode 120000 index 000000000..a61630ef4 --- /dev/null +++ b/sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/q2/82/MD5E-s1103696--c17e46fd78acd96dc3a59b36e51aa392.nii.gz/MD5E-s1103696--c17e46fd78acd96dc3a59b36e51aa392.nii.gz \ No newline at end of file diff --git a/sub-01/ses-013/sub-01_ses-013_scans.tsv b/sub-01/ses-013/sub-01_ses-013_scans.tsv new file mode 120000 index 000000000..1aa74277f --- /dev/null +++ b/sub-01/ses-013/sub-01_ses-013_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/3G/G6/MD5E-s2045--23b199ef363439ffd4ffd0dc0cebb492.tsv/MD5E-s2045--23b199ef363439ffd4ffd0dc0cebb492.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..aeb213e53 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.992768, 0.12003, 0.00221384, -0.111883, 0.931757, -0.345415], + "ImageOrientationText": "Tra>Cor(-20.1)>Sag(2.5)", + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0582855, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [608, -7198, -8822, 640, 90, 7, -71, 12], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 274.534, + "dcmmeta_affine": [ + [-1.9855356216430664, -0.22376617789268494, 0.08704576641321182, 113.15704345703125], + [-0.24005970358848572, 1.863513469696045, -0.68533855676651, -48.019012451171875], + [0.0044276840053498745, 0.6908301711082458, 1.8768948316574097, -60.511680603027344], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From f34ef4106eaf7b3c110861a0eec6f6515d3bc2f6 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:44:00 -0400 Subject: [PATCH 145/463] fill IntendedFor --- ...1_ses-025_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...1_ses-025_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-025_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...1_ses-025_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_epi.json index 2ab81fd30..1763a2e0c 100644 --- a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993707, - 0.105658, - 0.0371847, - -0.0839679, - 0.922394, - -0.377014 - ], + "ImageOrientationPatientDICOM": [0.993707, 0.105658, 0.0371847, -0.0839679, 0.922394, -0.377014], "ImageOrientationText": "Tra>Cor(-21.9)>Sag(4.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-025/func/sub-01_ses-025_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-025/func/sub-01_ses-025_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-025/func/sub-01_ses-025_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 623, - -7233, - -8805, - 589, - 178, - -29, - -117, - 89 - ], + "ShimSetting": [623, -7233, -8805, 589, 178, -29, -117, 89], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_epi.json index f7fe77278..07eb2f62a 100644 --- a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993707, - 0.105658, - 0.0371847, - -0.0839679, - 0.922394, - -0.377014 - ], + "ImageOrientationPatientDICOM": [0.993707, 0.105658, 0.0371847, -0.0839679, 0.922394, -0.377014], "ImageOrientationText": "Tra>Cor(-21.9)>Sag(4.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-025/func/sub-01_ses-025_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 623, - -7233, - -8805, - 589, - 178, - -29, - -117, - 89 - ], + "ShimSetting": [623, -7233, -8805, 589, 178, -29, -117, 89], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_epi.json index 9d27c1343..26b334a05 100644 --- a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993707, - 0.105658, - 0.0371847, - -0.0839679, - 0.922394, - -0.377014 - ], + "ImageOrientationPatientDICOM": [0.993707, 0.105658, 0.0371847, -0.0839679, 0.922394, -0.377014], "ImageOrientationText": "Tra>Cor(-21.9)>Sag(4.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-025/func/sub-01_ses-025_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 623, - -7233, - -8805, - 589, - 178, - -29, - -117, - 89 - ], + "ShimSetting": [623, -7233, -8805, 589, 178, -29, -117, 89], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_epi.json b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_epi.json index 0f9a9b617..dca27ce51 100644 --- a/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-01/ses-025/fmap/sub-01_ses-025_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.993707, - 0.105658, - 0.0371847, - -0.0839679, - 0.922394, - -0.377014 - ], + "ImageOrientationPatientDICOM": [0.993707, 0.105658, 0.0371847, -0.0839679, 0.922394, -0.377014], "ImageOrientationText": "Tra>Cor(-21.9)>Sag(4.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-025/func/sub-01_ses-025_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 623, - -7233, - -8805, - 589, - 178, - -29, - -117, - 89 - ], + "ShimSetting": [623, -7233, -8805, 589, 178, -29, -117, 89], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 2aeb855c95e48579580b3a4c7524b8da5d8b7f79 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:44:18 -0400 Subject: [PATCH 146/463] fix fmap phase --- ...2_ses-015_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-015_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-015_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-015_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-015_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-015_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-015_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-02/ses-015/sub-02_ses-015_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-02/ses-015/fmap/{sub-02_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-015_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-015/fmap/{sub-02_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-015_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-015/fmap/{sub-02_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-015_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-015/fmap/{sub-02_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-015_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-015/fmap/{sub-02_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-015_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-015/fmap/{sub-02_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-015_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-015/fmap/{sub-02_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-015_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-015/fmap/{sub-02_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-015_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-015/fmap/{sub-02_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-015_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-015/fmap/{sub-02_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-015_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-02/ses-015/fmap/{sub-02_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-02_ses-015_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-02/ses-015/fmap/{sub-02_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-02_ses-015_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 29d53736b..000000000 --- a/sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:10:16.340000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.99935, 0.00491479, 0.0357229, 0.0151757, 0.84134, -0.540293], - "ImageOrientationText": "Tra>Cor(-32.7)>Sag(1.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0563409, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [614, -7191, -8860, 215, 49, -213, -28, 49], - "SliceThickness": 2, - "SliceTiming": [0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 308.032, - "WipMemBlock": "5e3d94f9-99ae-4eef-bedf-1e199e91e701||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9986993074417114, 0.030351394787430763, 0.06542108952999115, 104.5475082397461], - [-0.00982957985252142, 1.6826802492141724, -1.0809675455093384, -47.32787322998047], - [0.07144582271575928, 1.0805859565734863, 1.6814367771148682, -87.17710876464844], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99934964780476, 0.00491478991379, 0.0357229096324, 0.01517569775208, 0.84134010418048, -0.5402930013385], - "ImagePositionPatient": [-846.24815055261, -742.06175209273, 391.45027886963], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.260288, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "160824.658000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.05634088253834, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "161103.011000", - "SliceLocation": -44.29164186076, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000349439, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "160824.588000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["161016.340000", "161017.830000", "161019.320000"], - "ContentTime": ["161103.013000", "161103.016000", "161103.019000"], - "InstanceCreationTime": ["161103.013000", "161103.016000", "161103.019000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4708.0, 4700.0, 4712.0], - "WindowWidth": [18510.0, 18508.0, 18512.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index b41189bc0..000000000 --- a/sub-02/ses-015/fmap/sub-02_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/84/6g/MD5E-s3334001--f97b61eb28caba0240fb42017ffd6458.nii.gz/MD5E-s3334001--f97b61eb28caba0240fb42017ffd6458.nii.gz \ No newline at end of file diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index af88c329e..000000000 --- a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:10:5.910000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99935, - 0.00491479, - 0.0357229, - 0.0151757, - 0.84134, - -0.540293 - ], - "ImageOrientationText": "Tra>Cor(-32.7)>Sag(1.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0563409, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 614, - -7191, - -8860, - 215, - 49, - -213, - -28, - 49 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 308.032, - "WipMemBlock": "5e3d94f9-99ae-4eef-bedf-1e199e91e701||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 1ee8be0bd..000000000 --- a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Jz/9G/MD5E-s1112091--39a8615730925b1ffe88c1e71f839739.nii.gz/MD5E-s1112091--39a8615730925b1ffe88c1e71f839739.nii.gz \ No newline at end of file diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 7897288d9..000000000 --- a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:11:18.500000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99935, - 0.00491479, - 0.0357229, - 0.0151757, - 0.84134, - -0.540293 - ], - "ImageOrientationText": "Tra>Cor(-32.7)>Sag(1.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0706465, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 614, - -7191, - -8860, - 215, - 49, - -213, - -28, - 49 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 308.032, - "WipMemBlock": "51b282d1-e9b7-4d63-85af-a74d95a9d51a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index d4c5276c5..000000000 --- a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/W4/4M/MD5E-s1103185--ec4fef196588602b0ed10906f9b23309.nii.gz/MD5E-s1103185--ec4fef196588602b0ed10906f9b23309.nii.gz \ No newline at end of file diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index ce87b56ce..000000000 --- a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:19:37.210000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99935, - 0.00491479, - 0.0357229, - 0.0151757, - 0.84134, - -0.540293 - ], - "ImageOrientationText": "Tra>Cor(-32.7)>Sag(1.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0706465, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 614, - -7191, - -8860, - 215, - 49, - -213, - -28, - 49 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 308.032, - "WipMemBlock": "13929814-bb54-4731-9492-7a09d1e9f4c4||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index ce0c42c87..000000000 --- a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/VM/pX/MD5E-s1103397--f9c38dd5fce49858565e26aa1d6938f1.nii.gz/MD5E-s1103397--f9c38dd5fce49858565e26aa1d6938f1.nii.gz \ No newline at end of file diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index d1a8956b2..000000000 --- a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:32:13.397500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99935, - 0.00491479, - 0.0357229, - 0.0151757, - 0.84134, - -0.540293 - ], - "ImageOrientationText": "Tra>Cor(-32.7)>Sag(1.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0706465, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 614, - -7191, - -8860, - 215, - 49, - -213, - -28, - 49 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 308.032, - "WipMemBlock": "0338b437-28c6-4790-9253-b58d53f0d7f4||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index e7bf1330a..000000000 --- a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Mf/g4/MD5E-s1103356--e271a959e8573e4ffcba2942fdf36812.nii.gz/MD5E-s1103356--e271a959e8573e4ffcba2942fdf36812.nii.gz \ No newline at end of file diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index e01c2a290..000000000 --- a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:40:46.325000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99935, - 0.00491479, - 0.0357229, - 0.0151757, - 0.84134, - -0.540293 - ], - "ImageOrientationText": "Tra>Cor(-32.7)>Sag(1.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0706465, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 614, - -7191, - -8860, - 215, - 49, - -213, - -28, - 49 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 308.032, - "WipMemBlock": "20a054f8-aaa2-4103-8a73-9bf739a9fb49||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index a0bba2cbb..000000000 --- a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/fp/kv/MD5E-s1103487--75e7261337bb2f761447f317fa2ef40a.nii.gz/MD5E-s1103487--75e7261337bb2f761447f317fa2ef40a.nii.gz \ No newline at end of file diff --git a/sub-02/ses-015/sub-02_ses-015_scans.tsv b/sub-02/ses-015/sub-02_ses-015_scans.tsv index 91a9792d3..87b1e69cc 120000 --- a/sub-02/ses-015/sub-02_ses-015_scans.tsv +++ b/sub-02/ses-015/sub-02_ses-015_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/m4/jG/MD5E-s3289--d1a7d1d3c3aa872371d414f455360957.tsv/MD5E-s3289--d1a7d1d3c3aa872371d414f455360957.tsv \ No newline at end of file +../../.git/annex/objects/23/K3/MD5E-s2567--9a028c91013ce5a19ee4e82ddbc04f6d.tsv/MD5E-s2567--9a028c91013ce5a19ee4e82ddbc04f6d.tsv \ No newline at end of file From 280d04a064822f821f17b5718cc9755f3dd00575 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:44:29 -0400 Subject: [PATCH 147/463] fix fmap phase --- ...1_ses-013_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-013_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-013_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-013_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-013_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-013_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-013_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-013_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - sub-01/ses-013/sub-01_ses-013_scans.tsv | 2 +- 17 files changed, 1 insertion(+), 638 deletions(-) rename sub-01/ses-013/fmap/{sub-01_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-013_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-013/fmap/{sub-01_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-013_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-013/fmap/{sub-01_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-013_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-013/fmap/{sub-01_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-013_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-013/fmap/{sub-01_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-013_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-013/fmap/{sub-01_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-013_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-013/fmap/{sub-01_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-013_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-013/fmap/{sub-01_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-013_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 687cf0ead..000000000 --- a/sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:35:53.850000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.992768, 0.12003, 0.00221384, -0.111883, 0.931757, -0.345415], - "ImageOrientationText": "Tra>Cor(-20.1)>Sag(2.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - 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1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 274.534, - "WipMemBlock": "f040b746-fafe-4e36-9c94-47b8e7d600f2||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9855356216430664, -0.22376617789268494, 0.08704576641321182, 113.15704345703125], - [-0.24005970358848572, 1.863513469696045, -0.68533855676651, -48.019012451171875], - [0.0044276840053498745, 0.6908301711082458, 1.8768948316574097, -60.511680603027344], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99276781462423, 0.12002985107661, 0.00221384207894, -0.1118830856221, 0.93175672431547, -0.3454150863014], - "ImagePositionPatient": [-731.3932074, -909.62349813954, 260.49433431722], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.260274, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "113353.794000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.04648288058663, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "113640.503000", - "SliceLocation": -35.407465828027, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999902526, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "113353.727000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["113553.850000", "113555.340000", "113556.830000"], - "ContentTime": ["113640.505000", "113640.511000", "113640.514000"], - "InstanceCreationTime": ["113640.505000", "113640.511000", "113640.514000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4790.0, 4790.0, 4784.0], - "WindowWidth": [18560.0, 18556.0, 18562.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 1582155e6..000000000 --- a/sub-01/ses-013/fmap/sub-01_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/6J/q6/MD5E-s3335473--818a148b0b5578dead2e26f0af8e71c7.nii.gz/MD5E-s3335473--818a148b0b5578dead2e26f0af8e71c7.nii.gz \ No newline at end of file diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 80a677946..000000000 --- a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:35:43.420000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992768, - 0.12003, - 0.00221384, - -0.111883, - 0.931757, - -0.345415 - ], - "ImageOrientationText": "Tra>Cor(-20.1)>Sag(2.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - 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"TotalReadoutTime": 0.0576811, - "TxRefAmp": 274.534, - "WipMemBlock": "f040b746-fafe-4e36-9c94-47b8e7d600f2||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 372010ce6..000000000 --- a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/8P/w1/MD5E-s1112376--305acea7c2ab354eac4effb708d9d431.nii.gz/MD5E-s1112376--305acea7c2ab354eac4effb708d9d431.nii.gz \ No newline at end of file diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 8740683ec..000000000 --- a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:37:29.532500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992768, - 0.12003, - 0.00221384, - -0.111883, - 0.931757, - -0.345415 - ], - "ImageOrientationText": "Tra>Cor(-20.1)>Sag(2.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0582855, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 608, - -7198, - -8822, - 640, - 90, - 7, - -71, - 12 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 274.534, - "WipMemBlock": "57ccf557-d382-44f6-9210-ed3c5629d762||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 5f783d4d5..000000000 --- a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/41/vM/MD5E-s1103581--0a6f8af5ee0921e72c473982adbcc6b2.nii.gz/MD5E-s1103581--0a6f8af5ee0921e72c473982adbcc6b2.nii.gz \ No newline at end of file diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 1d947b3d4..000000000 --- a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:47:55.747500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992768, - 0.12003, - 0.00221384, - -0.111883, - 0.931757, - -0.345415 - ], - "ImageOrientationText": "Tra>Cor(-20.1)>Sag(2.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0582855, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 608, - -7198, - -8822, - 640, - 90, - 7, - -71, - 12 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 274.534, - "WipMemBlock": "1a6718dc-a04b-4556-a4b6-c668b5fe3bab||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index a61630ef4..000000000 --- a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/q2/82/MD5E-s1103696--c17e46fd78acd96dc3a59b36e51aa392.nii.gz/MD5E-s1103696--c17e46fd78acd96dc3a59b36e51aa392.nii.gz \ No newline at end of file diff --git a/sub-01/ses-013/sub-01_ses-013_scans.tsv b/sub-01/ses-013/sub-01_ses-013_scans.tsv index 1aa74277f..a08118d14 120000 --- a/sub-01/ses-013/sub-01_ses-013_scans.tsv +++ b/sub-01/ses-013/sub-01_ses-013_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/3G/G6/MD5E-s2045--23b199ef363439ffd4ffd0dc0cebb492.tsv/MD5E-s2045--23b199ef363439ffd4ffd0dc0cebb492.tsv \ No newline at end of file +../../.git/annex/objects/9p/xz/MD5E-s1565--eead05f17426eef7abb0369266e41086.tsv/MD5E-s1565--eead05f17426eef7abb0369266e41086.tsv \ No newline at end of file From df7899e70d24b852f9e3d9c1cea11bead5472374 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:44:29 -0400 Subject: [PATCH 148/463] fix complex event files --- ...g_events.tsv => sub-02_ses-015_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-02_ses-015_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-02_ses-015_task-mario3_run-03_events.tsv} | 0 .../func/sub-02_ses-015_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-02_ses-015_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-02_ses-015_task-mario3_run-04_events.tsv} | 0 .../func/sub-02_ses-015_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-02_ses-015_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-02/ses-015/func/{sub-02_ses-015_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-015_task-mario3_run-01_events.tsv} (100%) rename sub-02/ses-015/func/{sub-02_ses-015_task-mario3_run-01_part-phase_events.tsv => sub-02_ses-015_task-mario3_run-02_events.tsv} (100%) rename sub-02/ses-015/func/{sub-02_ses-015_task-mario3_run-02_part-mag_events.tsv => sub-02_ses-015_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_part-phase_events.tsv rename sub-02/ses-015/func/{sub-02_ses-015_task-mario3_run-02_part-phase_events.tsv => sub-02_ses-015_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-02_events.tsv similarity index 100% rename from sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-01_part-phase_events.tsv rename to sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-02_events.tsv diff --git a/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-02_part-mag_events.tsv b/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_events.tsv similarity index 100% rename from sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-02_part-mag_events.tsv rename to sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_events.tsv diff --git a/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_part-mag_events.tsv b/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-02_part-phase_events.tsv b/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_events.tsv similarity index 100% rename from sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-02_part-phase_events.tsv rename to sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_events.tsv diff --git a/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_part-mag_events.tsv b/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_part-phase_events.tsv b/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-015/func/sub-02_ses-015_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From d6252240d3810b911ec887f8c1c08b3ca9e56458 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:44:38 -0400 Subject: [PATCH 149/463] fix complex event files --- ...g_events.tsv => sub-01_ses-013_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-013_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-013_task-mario3_run-02_part-mag_events.tsv | 1 - .../func/sub-01_ses-013_task-mario3_run-02_part-phase_events.tsv | 1 - 4 files changed, 2 deletions(-) rename sub-01/ses-013/func/{sub-01_ses-013_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-013_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-013/func/{sub-01_ses-013_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-013_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-mag_events.tsv delete mode 120000 sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-phase_events.tsv diff --git a/sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-013/func/sub-01_ses-013_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From bb836d62846d0c98bb07bcf9df3b682b9812726b Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:45:04 -0400 Subject: [PATCH 150/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..b245b94cf --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = fe7d3d27-c164-4d8f-8372-f92a1c2ab719 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..593962574 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 593962574e1f6a5f6d45283440b555bed07c437f From fd17aeb760038246eaaf5e337c833c80a0dd2ba9 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:45:31 -0400 Subject: [PATCH 151/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-006_acq-axial_localizer.json | 81 +++ .../sub-02_ses-006_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-006_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-006_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-006_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-006_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-006/anat/sub-02_ses-006_scout.json | 542 ++++++++++++++++++ .../ses-006/anat/sub-02_ses-006_scout.nii.gz | 1 + ...6_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-006_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...06_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...006_task-mario3_run-01_part-mag_events.tsv | 1 + ...006_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-01_part-phase_events.tsv | 1 + ...6_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-006_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...06_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...006_task-mario3_run-02_part-mag_events.tsv | 1 + ...006_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-02_part-phase_events.tsv | 1 + ...6_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-006_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...06_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...006_task-mario3_run-03_part-mag_events.tsv | 1 + ...006_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-03_part-phase_events.tsv | 1 + ...6_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-02/ses-006/sub-02_ses-006_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-006/anat/sub-02_ses-006_acq-axial_localizer.json create mode 120000 sub-02/ses-006/anat/sub-02_ses-006_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-006/anat/sub-02_ses-006_acq-coronal_localizer.json create mode 120000 sub-02/ses-006/anat/sub-02_ses-006_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-006/anat/sub-02_ses-006_acq-sagittal_localizer.json create mode 120000 sub-02/ses-006/anat/sub-02_ses-006_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-006/anat/sub-02_ses-006_scout.json create mode 120000 sub-02/ses-006/anat/sub-02_ses-006_scout.nii.gz create mode 100644 sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-02/ses-006/sub-02_ses-006_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 593962574..c2ffdbf75 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 593962574e1f6a5f6d45283440b555bed07c437f +Subproject commit c2ffdbf7594aa381e4043ec418afe0e087254c8f diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..83ada7a9d --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 51 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-006/anat/sub-02_ses-006_acq-axial_localizer.json b/sub-02/ses-006/anat/sub-02_ses-006_acq-axial_localizer.json new file mode 100644 index 000000000..e2802b0d7 --- /dev/null +++ b/sub-02/ses-006/anat/sub-02_ses-006_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:23:18.087500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0549023, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 330.264 +} \ No newline at end of file diff --git a/sub-02/ses-006/anat/sub-02_ses-006_acq-axial_localizer.nii.gz b/sub-02/ses-006/anat/sub-02_ses-006_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..6f9405829 --- /dev/null +++ b/sub-02/ses-006/anat/sub-02_ses-006_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/3f/8P/MD5E-s180887--cef13f512b2621b1ec2da8b7900bcf15.nii.gz/MD5E-s180887--cef13f512b2621b1ec2da8b7900bcf15.nii.gz \ No newline at end of file diff --git a/sub-02/ses-006/anat/sub-02_ses-006_acq-coronal_localizer.json b/sub-02/ses-006/anat/sub-02_ses-006_acq-coronal_localizer.json new file mode 100644 index 000000000..683d020ae --- /dev/null +++ b/sub-02/ses-006/anat/sub-02_ses-006_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:23:25.077500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + 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4.705, + 4.8025, + 4.9, + 4.9975, + 5.0975, + 5.195, + 5.2925, + 5.39, + 5.4875, + 5.5875, + 5.685, + 5.7825 + ], + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 330.264, + "WipMemBlock": "f5941d4a-0b21-40d1-b43c-ffc640ea79ea||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-phase_sbref.nii.gz b/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-phase_sbref.nii.gz new file mode 120000 index 000000000..cdb7ac0d7 --- /dev/null +++ b/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/gQ/pK/MD5E-s1103346--7fd8edba494664b10a143aba020ce7cc.nii.gz/MD5E-s1103346--7fd8edba494664b10a143aba020ce7cc.nii.gz \ No newline at end of file diff --git a/sub-02/ses-006/sub-02_ses-006_scans.tsv b/sub-02/ses-006/sub-02_ses-006_scans.tsv new file mode 120000 index 000000000..8096369fd --- /dev/null +++ b/sub-02/ses-006/sub-02_ses-006_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/mg/W5/MD5E-s2667--81d3af356b4a7620a059ca885a864509.tsv/MD5E-s2667--81d3af356b4a7620a059ca885a864509.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..d1be66a9d --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999254, -0.00157163, 0.0385826, 0.0228508, 0.82951, -0.558025], + "ImageOrientationText": "Tra>Cor(-34.0)>Sag(1.8)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0808656, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [623, -7169, -8876, 227, 39, -246, -50, 34], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 330.264, + "dcmmeta_affine": [ + [-1.998508334159851, 0.045701541006565094, 0.06225527077913284, 103.65025329589844], + [0.0031432537361979485, 1.6590192317962646, -1.1169804334640503, -46.377525329589844], + [0.07716520875692368, 1.1160495281219482, 1.6578538417816162, -105.1323471069336], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 77a90fedc5c39a60b448d2e40cb875f5cf040878 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:45:33 -0400 Subject: [PATCH 152/463] fill IntendedFor --- ...1_ses-013_acq-sbref_dir-AP_run-01_epi.json | 89 ++----------------- ...1_ses-013_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-013_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- 3 files changed, 22 insertions(+), 243 deletions(-) diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_epi.json index 371dbb449..57ade55e8 100644 --- a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992768, - 0.12003, - 0.00221384, - -0.111883, - 0.931757, - -0.345415 - ], + "ImageOrientationPatientDICOM": [0.992768, 0.12003, 0.00221384, -0.111883, 0.931757, -0.345415], "ImageOrientationText": "Tra>Cor(-20.1)>Sag(2.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,16 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-013/func/sub-01_ses-013_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-013/func/sub-01_ses-013_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +64,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 608, - -7198, - -8822, - 640, - 90, - 7, - -71, - 12 - ], + "ShimSetting": [608, -7198, -8822, 640, 90, 7, -71, 12], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_epi.json index 745fd0fc1..817a7ee7a 100644 --- a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992768, - 0.12003, - 0.00221384, - -0.111883, - 0.931757, - -0.345415 - ], + "ImageOrientationPatientDICOM": [0.992768, 0.12003, 0.00221384, -0.111883, 0.931757, -0.345415], "ImageOrientationText": "Tra>Cor(-20.1)>Sag(2.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-013/func/sub-01_ses-013_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 608, - -7198, - -8822, - 640, - 90, - 7, - -71, - 12 - ], + "ShimSetting": [608, -7198, -8822, 640, 90, 7, -71, 12], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_epi.json index 8882c1578..750123c9b 100644 --- a/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-013/fmap/sub-01_ses-013_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.992768, - 0.12003, - 0.00221384, - -0.111883, - 0.931757, - -0.345415 - ], + "ImageOrientationPatientDICOM": [0.992768, 0.12003, 0.00221384, -0.111883, 0.931757, -0.345415], "ImageOrientationText": "Tra>Cor(-20.1)>Sag(2.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-013/func/sub-01_ses-013_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 608, - -7198, - -8822, - 640, - 90, - 7, - -71, - 12 - ], + "ShimSetting": [608, -7198, -8822, 640, 90, 7, -71, 12], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 5e3e296898c57a1649ba92d57bf0c709d430c494 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:45:35 -0400 Subject: [PATCH 153/463] fill IntendedFor --- ...2_ses-015_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...2_ses-015_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...2_ses-015_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...2_ses-015_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...2_ses-015_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_epi.json index 32e523b9d..7bacdb76a 100644 --- a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99935, - 0.00491479, - 0.0357229, - 0.0151757, - 0.84134, - -0.540293 - ], + "ImageOrientationPatientDICOM": [0.99935, 0.00491479, 0.0357229, 0.0151757, 0.84134, -0.540293], "ImageOrientationText": "Tra>Cor(-32.7)>Sag(1.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-02_ses-015_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-015/func/sub-02_ses-015_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-015/func/sub-02_ses-015_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-015/func/sub-02_ses-015_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 614, - -7191, - -8860, - 215, - 49, - -213, - -28, - 49 - ], + "ShimSetting": [614, -7191, -8860, 215, 49, -213, -28, 49], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_epi.json b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_epi.json index 399a8f7df..71a7972f4 100644 --- a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99935, - 0.00491479, - 0.0357229, - 0.0151757, - 0.84134, - -0.540293 - ], + "ImageOrientationPatientDICOM": [0.99935, 0.00491479, 0.0357229, 0.0151757, 0.84134, -0.540293], "ImageOrientationText": "Tra>Cor(-32.7)>Sag(1.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-02_ses-015_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 614, - -7191, - -8860, - 215, - 49, - -213, - -28, - 49 - ], + "ShimSetting": [614, -7191, -8860, 215, 49, -213, -28, 49], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_epi.json b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_epi.json index 76cb8c3b0..238149377 100644 --- a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99935, - 0.00491479, - 0.0357229, - 0.0151757, - 0.84134, - -0.540293 - ], + "ImageOrientationPatientDICOM": [0.99935, 0.00491479, 0.0357229, 0.0151757, 0.84134, -0.540293], "ImageOrientationText": "Tra>Cor(-32.7)>Sag(1.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-02_ses-015_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 614, - -7191, - -8860, - 215, - 49, - -213, - -28, - 49 - ], + "ShimSetting": [614, -7191, -8860, 215, 49, -213, -28, 49], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_epi.json b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_epi.json index 1a6715d89..821f03e73 100644 --- a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99935, - 0.00491479, - 0.0357229, - 0.0151757, - 0.84134, - -0.540293 - ], + "ImageOrientationPatientDICOM": [0.99935, 0.00491479, 0.0357229, 0.0151757, 0.84134, -0.540293], "ImageOrientationText": "Tra>Cor(-32.7)>Sag(1.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-02_ses-015_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 614, - -7191, - -8860, - 215, - 49, - -213, - -28, - 49 - ], + "ShimSetting": [614, -7191, -8860, 215, 49, -213, -28, 49], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_epi.json b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_epi.json index 90c9300cc..8c6aec306 100644 --- a/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-02/ses-015/fmap/sub-02_ses-015_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99935, - 0.00491479, - 0.0357229, - 0.0151757, - 0.84134, - -0.540293 - ], + "ImageOrientationPatientDICOM": [0.99935, 0.00491479, 0.0357229, 0.0151757, 0.84134, -0.540293], "ImageOrientationText": "Tra>Cor(-32.7)>Sag(1.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-02_ses-015_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 614, - -7191, - -8860, - 215, - 49, - -213, - -28, - 49 - ], + "ShimSetting": [614, -7191, -8860, 215, 49, -213, -28, 49], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From a7a83e24912f399b9feabf2abd7e0a7499bf4732 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:46:12 -0400 Subject: [PATCH 154/463] fix fmap phase --- ...2_ses-006_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-006_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-006_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-02/ses-006/sub-02_ses-006_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-02/ses-006/fmap/{sub-02_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-006_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-006/fmap/{sub-02_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-006_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-006/fmap/{sub-02_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-006_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-006/fmap/{sub-02_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-006_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-006/fmap/{sub-02_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-006_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-006/fmap/{sub-02_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-006_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-006/fmap/{sub-02_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-006_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-006/fmap/{sub-02_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-006_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-006/fmap/{sub-02_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-006_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-006/fmap/{sub-02_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-006_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 8640bbc38..000000000 --- a/sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:24:22.372500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - 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["112422.372500", "112423.862500", "112425.352500"], - "ContentTime": ["112508.686000", "112508.688000", "112508.691000"], - "InstanceCreationTime": ["112508.686000", "112508.688000", "112508.691000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4756.0, 4756.0, 4760.0], - "WindowWidth": [18544.0, 18540.0, 18534.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index db62c2449..000000000 --- a/sub-02/ses-006/fmap/sub-02_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/GX/m0/MD5E-s3333534--9689c6f2ce84938216e6a81e4022a6ea.nii.gz/MD5E-s3333534--9689c6f2ce84938216e6a81e4022a6ea.nii.gz \ No newline at end of file diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 6a63648fb..000000000 --- a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:24:11.942500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999254, - -0.00157163, - 0.0385826, - 0.0228508, - 0.82951, - -0.558025 - ], - "ImageOrientationText": "Tra>Cor(-34.0)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0644906, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": 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r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 61dd5ccb9..000000000 --- a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/xJ/8M/MD5E-s1112166--c457b49f5f549fceaa85bb21942f78fe.nii.gz/MD5E-s1112166--c457b49f5f549fceaa85bb21942f78fe.nii.gz \ No newline at end of file diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 93767e3e3..000000000 --- a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:30:23.335000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999254, - -0.00157163, - 0.0385826, - 0.0228508, - 0.82951, - -0.558025 - ], - "ImageOrientationText": "Tra>Cor(-34.0)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0808656, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 623, - -7169, - -8876, - 227, - 39, - -246, - -50, - 34 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 330.264, - "WipMemBlock": "62999c95-adc1-401a-b31a-8f89fd6a3609||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index d236eba9d..000000000 --- a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/8G/J1/MD5E-s1103325--cfa077c4707a89efc1915a0c6f5ae0c4.nii.gz/MD5E-s1103325--cfa077c4707a89efc1915a0c6f5ae0c4.nii.gz \ No newline at end of file diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 24008051d..000000000 --- a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:38:47.782500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999254, - -0.00157163, - 0.0385826, - 0.0228508, - 0.82951, - -0.558025 - ], - "ImageOrientationText": "Tra>Cor(-34.0)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0808656, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 623, - -7169, - -8876, - 227, - 39, - -246, - -50, - 34 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 330.264, - "WipMemBlock": "3e270137-6b3b-4254-b314-d093a833ddba||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 4caf26ff9..000000000 --- a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/98/5Z/MD5E-s1103332--cce887b868c78fa86636f11da10b0a6a.nii.gz/MD5E-s1103332--cce887b868c78fa86636f11da10b0a6a.nii.gz \ No newline at end of file diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 9a6718c57..000000000 --- a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:47:46.200000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999254, - -0.00157163, - 0.0385826, - 0.0228508, - 0.82951, - -0.558025 - ], - "ImageOrientationText": "Tra>Cor(-34.0)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0808656, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 623, - -7169, - -8876, - 227, - 39, - -246, - -50, - 34 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 330.264, - "WipMemBlock": "f5941d4a-0b21-40d1-b43c-ffc640ea79ea||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index cdb7ac0d7..000000000 --- a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/gQ/pK/MD5E-s1103346--7fd8edba494664b10a143aba020ce7cc.nii.gz/MD5E-s1103346--7fd8edba494664b10a143aba020ce7cc.nii.gz \ No newline at end of file diff --git a/sub-02/ses-006/sub-02_ses-006_scans.tsv b/sub-02/ses-006/sub-02_ses-006_scans.tsv index 8096369fd..387e31039 120000 --- a/sub-02/ses-006/sub-02_ses-006_scans.tsv +++ b/sub-02/ses-006/sub-02_ses-006_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/mg/W5/MD5E-s2667--81d3af356b4a7620a059ca885a864509.tsv/MD5E-s2667--81d3af356b4a7620a059ca885a864509.tsv \ No newline at end of file +../../.git/annex/objects/kF/wQ/MD5E-s2066--03cedc51261f5173cefe9c391deed3d0.tsv/MD5E-s2066--03cedc51261f5173cefe9c391deed3d0.tsv \ No newline at end of file From da3410c5eb8fde2b60852e7b203def91fd7f345c Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:46:23 -0400 Subject: [PATCH 155/463] fix complex event files --- ...g_events.tsv => sub-02_ses-006_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-02_ses-006_task-mario3_run-02_events.tsv} | 0 .../func/sub-02_ses-006_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-02_ses-006_task-mario3_run-03_events.tsv} | 0 .../func/sub-02_ses-006_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-02_ses-006_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-02/ses-006/func/{sub-02_ses-006_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-006_task-mario3_run-01_events.tsv} (100%) rename sub-02/ses-006/func/{sub-02_ses-006_task-mario3_run-01_part-phase_events.tsv => sub-02_ses-006_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_part-phase_events.tsv rename sub-02/ses-006/func/{sub-02_ses-006_task-mario3_run-02_part-mag_events.tsv => sub-02_ses-006_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_events.tsv similarity index 100% rename from sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_part-phase_events.tsv rename to sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_events.tsv diff --git a/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_part-phase_events.tsv b/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_part-mag_events.tsv b/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_events.tsv similarity index 100% rename from sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_part-mag_events.tsv rename to sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_events.tsv diff --git a/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-mag_events.tsv b/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 4f512474590a31c861dbaa4c321cc0308edf8957 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:46:34 -0400 Subject: [PATCH 156/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-021_acq-axial_localizer.json | 81 +++ .../sub-01_ses-021_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-021_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-021_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-021_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-021_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-021/anat/sub-01_ses-021_scout.json | 542 ++++++++++++++++++ .../ses-021/anat/sub-01_ses-021_scout.nii.gz | 1 + ...1_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-021_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...21_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...021_task-mario3_run-01_part-mag_events.tsv | 1 + ...021_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...21_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-01_part-phase_events.tsv | 1 + ...1_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-021_task-mario3_run-02_part-mag_bold.json | 500 ++++++++++++++++ ...21_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...021_task-mario3_run-02_part-mag_events.tsv | 1 + ...021_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...21_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-02_part-phase_events.tsv | 1 + ...1_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-021_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...21_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...021_task-mario3_run-03_part-mag_events.tsv | 1 + ...021_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...21_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-03_part-phase_events.tsv | 1 + ...1_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-021_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...21_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...021_task-mario3_run-04_part-mag_events.tsv | 1 + ...021_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...21_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-04_part-phase_events.tsv | 1 + ...1_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-01/ses-021/sub-01_ses-021_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5737 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-021/anat/sub-01_ses-021_acq-axial_localizer.json create mode 120000 sub-01/ses-021/anat/sub-01_ses-021_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-021/anat/sub-01_ses-021_acq-coronal_localizer.json create mode 120000 sub-01/ses-021/anat/sub-01_ses-021_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-021/anat/sub-01_ses-021_acq-sagittal_localizer.json create mode 120000 sub-01/ses-021/anat/sub-01_ses-021_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-021/anat/sub-01_ses-021_scout.json create mode 120000 sub-01/ses-021/anat/sub-01_ses-021_scout.nii.gz create mode 100644 sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_part-phase_sbref.nii.gz create mode 120000 sub-01/ses-021/sub-01_ses-021_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index d7a47ae21..53b7c51ee 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit d7a47ae21e971dc044006156fa5ef9fa76d1e182 +Subproject commit 53b7c51eec1d713e02efebe232ea9c1cbede6401 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-021/anat/sub-01_ses-021_acq-axial_localizer.json b/sub-01/ses-021/anat/sub-01_ses-021_acq-axial_localizer.json new file mode 100644 index 000000000..ae7e10bc5 --- /dev/null +++ b/sub-01/ses-021/anat/sub-01_ses-021_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:34:32.170000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + 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"ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0508668, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [610, -7247, -8814, 603, 116, -59, -54, 81], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 252.112, + "dcmmeta_affine": [ + [-1.9927266836166382, -0.10234203189611435, 0.13625892996788025, 109.39710235595703], + [-0.14392957091331482, 1.8669646978378296, -0.7026572823524475, -52.502567291259766], + [0.09123962372541428, 0.7099078297615051, 1.8675401210784912, -63.4535026550293], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 6109812cd841887c2d8b4c17c2d2eb536e210ad2 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:47:11 -0400 Subject: [PATCH 157/463] fill IntendedFor --- ...2_ses-006_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...2_ses-006_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...2_ses-006_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...2_ses-006_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_epi.json index 8bb1519f6..1edde1a57 100644 --- a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999254, - -0.00157163, - 0.0385826, - 0.0228508, - 0.82951, - -0.558025 - ], + "ImageOrientationPatientDICOM": [0.999254, -0.00157163, 0.0385826, 0.0228508, 0.82951, -0.558025], "ImageOrientationText": "Tra>Cor(-34.0)>Sag(1.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-02_ses-006_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-006/func/sub-02_ses-006_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-006/func/sub-02_ses-006_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 623, - -7169, - -8876, - 227, - 39, - -246, - -50, - 34 - ], + "ShimSetting": [623, -7169, -8876, 227, 39, -246, -50, 34], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.4875, 0.5875, 0.685, 0.7825, 0.88, 0.9775, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.485, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_epi.json b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_epi.json index 4a82b3c0e..487659610 100644 --- a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999254, - -0.00157163, - 0.0385826, - 0.0228508, - 0.82951, - -0.558025 - ], + "ImageOrientationPatientDICOM": [0.999254, -0.00157163, 0.0385826, 0.0228508, 0.82951, -0.558025], "ImageOrientationText": "Tra>Cor(-34.0)>Sag(1.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-02_ses-006_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 623, - -7169, - -8876, - 227, - 39, - -246, - -50, - 34 - ], + "ShimSetting": [623, -7169, -8876, 227, 39, -246, -50, 34], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_epi.json b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_epi.json index 0574eb25f..8fd2b6045 100644 --- a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999254, - -0.00157163, - 0.0385826, - 0.0228508, - 0.82951, - -0.558025 - ], + "ImageOrientationPatientDICOM": [0.999254, -0.00157163, 0.0385826, 0.0228508, 0.82951, -0.558025], "ImageOrientationText": "Tra>Cor(-34.0)>Sag(1.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-02_ses-006_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 623, - -7169, - -8876, - 227, - 39, - -246, - -50, - 34 - ], + "ShimSetting": [623, -7169, -8876, 227, 39, -246, -50, 34], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_epi.json b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_epi.json index 21ad37d4c..52ad96deb 100644 --- a/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-02/ses-006/fmap/sub-02_ses-006_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999254, - -0.00157163, - 0.0385826, - 0.0228508, - 0.82951, - -0.558025 - ], + "ImageOrientationPatientDICOM": [0.999254, -0.00157163, 0.0385826, 0.0228508, 0.82951, -0.558025], "ImageOrientationText": "Tra>Cor(-34.0)>Sag(1.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-02_ses-006_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 623, - -7169, - -8876, - 227, - 39, - -246, - -50, - 34 - ], + "ShimSetting": [623, -7169, -8876, 227, 39, -246, -50, 34], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 2a90354ae65f0be9103b7049c0c0eec916f9e973 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:47:16 -0400 Subject: [PATCH 158/463] fix fmap phase --- ...1_ses-021_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-021_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-021_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-021_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-021_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-021_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-021_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-021_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-021_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-021_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-021_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-021_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-01/ses-021/sub-01_ses-021_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-01/ses-021/fmap/{sub-01_ses-021_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-021_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-021/fmap/{sub-01_ses-021_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-021_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-021/fmap/{sub-01_ses-021_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-021_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-021/fmap/{sub-01_ses-021_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-021_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-021/fmap/{sub-01_ses-021_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-021_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-021/fmap/{sub-01_ses-021_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-021_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-021/fmap/{sub-01_ses-021_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-021_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-021/fmap/{sub-01_ses-021_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-021_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-01/ses-021/fmap/{sub-01_ses-021_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-01_ses-021_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-01/ses-021/fmap/{sub-01_ses-021_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-01_ses-021_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-01/ses-021/fmap/{sub-01_ses-021_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-01_ses-021_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-01/ses-021/fmap/{sub-01_ses-021_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-01_ses-021_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 4e685469f..000000000 --- a/sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:35:58.612500", - "BandwidthPerPixelPhaseEncode": 17.17, - 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b/sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 014831524..000000000 --- a/sub-01/ses-021/fmap/sub-01_ses-021_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/88/PV/MD5E-s3334718--f8ca266130db0e345abeb94d6da8b9ec.nii.gz/MD5E-s3334718--f8ca266130db0e345abeb94d6da8b9ec.nii.gz \ No newline at end of file diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 4bfccac06..000000000 --- a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:35:48.182500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 252.112, - "WipMemBlock": "140c7ea6-6fff-4d50-9c96-5eaad58e9680||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index f588ccc92..000000000 --- a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/7V/7K/MD5E-s1112115--726d6b4f0ddce693b645d8c5b643b6d2.nii.gz/MD5E-s1112115--726d6b4f0ddce693b645d8c5b643b6d2.nii.gz \ No newline at end of file diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index ba9d7c660..000000000 --- a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:39:5.440000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 252.112, - "WipMemBlock": "3decb948-b170-4070-84dd-2bb3f3ebc67b||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 6dc9a072d..000000000 --- a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Q4/jw/MD5E-s1103833--e34963d2bdce4786ad68d41b10fdd925.nii.gz/MD5E-s1103833--e34963d2bdce4786ad68d41b10fdd925.nii.gz \ No newline at end of file diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 576818bc5..000000000 --- a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:47:16.507500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996363, - 0.0719648, - 0.0456198, - -0.051171, - 0.933482, - -0.354954 - ], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(3.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0508668, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - 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"96d53eba-e263-4a9f-8860-47ca1fd41f5d||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 140e6086a..000000000 --- a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/4x/3p/MD5E-s1103797--d5ffcb2159b49c1ad91d049b4137588e.nii.gz/MD5E-s1103797--d5ffcb2159b49c1ad91d049b4137588e.nii.gz \ No newline at end of file diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index fc6e962aa..000000000 --- a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:56:35.975000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of 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b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 63269f0b9..000000000 --- a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/gq/Zj/MD5E-s1103805--0b7f31643265d2093fe173fb10b3ef79.nii.gz/MD5E-s1103805--0b7f31643265d2093fe173fb10b3ef79.nii.gz \ No newline at end of file diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 9cc019577..000000000 --- a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "12:06:44.225000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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"PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0508668, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 610, - -7247, - -8814, - 603, - 116, - -59, - -54, - 81 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 252.112, - "WipMemBlock": "4772617a-73f6-4166-ae0f-ba5c53b103ad||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 357cf613f..000000000 --- a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/PW/Vp/MD5E-s1103802--5d07f46b500e96a890a0e5b1e2c71a46.nii.gz/MD5E-s1103802--5d07f46b500e96a890a0e5b1e2c71a46.nii.gz \ No newline at end of file diff --git a/sub-01/ses-021/sub-01_ses-021_scans.tsv b/sub-01/ses-021/sub-01_ses-021_scans.tsv index 1ff59ef27..c5c3b7ec7 120000 --- a/sub-01/ses-021/sub-01_ses-021_scans.tsv +++ b/sub-01/ses-021/sub-01_ses-021_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/qK/wX/MD5E-s3289--9a52b2eed68b9fee227ebf380b737310.tsv/MD5E-s3289--9a52b2eed68b9fee227ebf380b737310.tsv \ No newline at end of file +../../.git/annex/objects/WZ/mZ/MD5E-s2567--e0d76977864c2aa8667223ab07679598.tsv/MD5E-s2567--e0d76977864c2aa8667223ab07679598.tsv \ No newline at end of file From 139401dec9e9b67e00df4970ae98f55cce2b47c9 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:47:24 -0400 Subject: [PATCH 159/463] fix complex event files --- ...g_events.tsv => sub-01_ses-021_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-021_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-01_ses-021_task-mario3_run-03_events.tsv} | 0 .../func/sub-01_ses-021_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-01_ses-021_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-01_ses-021_task-mario3_run-04_events.tsv} | 0 .../func/sub-01_ses-021_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-01_ses-021_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-01/ses-021/func/{sub-01_ses-021_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-021_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-021/func/{sub-01_ses-021_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-021_task-mario3_run-02_events.tsv} (100%) rename sub-01/ses-021/func/{sub-01_ses-021_task-mario3_run-02_part-mag_events.tsv => sub-01_ses-021_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_part-phase_events.tsv rename sub-01/ses-021/func/{sub-01_ses-021_task-mario3_run-02_part-phase_events.tsv => sub-01_ses-021_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_events.tsv similarity index 100% rename from sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-02_part-mag_events.tsv rename to sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_events.tsv diff --git a/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_part-mag_events.tsv b/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_events.tsv similarity index 100% rename from sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-02_part-phase_events.tsv rename to sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_events.tsv diff --git a/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_part-mag_events.tsv b/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_part-phase_events.tsv b/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-021/func/sub-01_ses-021_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 220b02e86352ded725b13f9c578647f1b84d2067 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:48:21 -0400 Subject: [PATCH 160/463] fill IntendedFor --- ...1_ses-021_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...1_ses-021_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-021_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...1_ses-021_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...1_ses-021_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_epi.json index 645104346..71b64090a 100644 --- a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996363, - 0.0719648, - 0.0456198, - -0.051171, - 0.933482, - -0.354954 - ], + "ImageOrientationPatientDICOM": [0.996363, 0.0719648, 0.0456198, -0.051171, 0.933482, -0.354954], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(3.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-021/func/sub-01_ses-021_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-021/func/sub-01_ses-021_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-021/func/sub-01_ses-021_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-021/func/sub-01_ses-021_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 610, - -7247, - -8814, - 603, - 116, - -59, - -54, - 81 - ], + "ShimSetting": [610, -7247, -8814, 603, 116, -59, -54, 81], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_epi.json index f7247776e..c08a6fcbf 100644 --- a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996363, - 0.0719648, - 0.0456198, - -0.051171, - 0.933482, - -0.354954 - ], + "ImageOrientationPatientDICOM": [0.996363, 0.0719648, 0.0456198, -0.051171, 0.933482, -0.354954], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(3.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-021/func/sub-01_ses-021_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 610, - -7247, - -8814, - 603, - 116, - -59, - -54, - 81 - ], + "ShimSetting": [610, -7247, -8814, 603, 116, -59, -54, 81], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.4875, 0.5875, 0.685, 0.7825, 0.88, 0.9775, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.485, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_epi.json index 37e12a1f5..234e1abb7 100644 --- a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996363, - 0.0719648, - 0.0456198, - -0.051171, - 0.933482, - -0.354954 - ], + "ImageOrientationPatientDICOM": [0.996363, 0.0719648, 0.0456198, -0.051171, 0.933482, -0.354954], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(3.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-021/func/sub-01_ses-021_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 610, - -7247, - -8814, - 603, - 116, - -59, - -54, - 81 - ], + "ShimSetting": [610, -7247, -8814, 603, 116, -59, -54, 81], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_epi.json b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_epi.json index e9dbaf54d..266efc4b7 100644 --- a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996363, - 0.0719648, - 0.0456198, - -0.051171, - 0.933482, - -0.354954 - ], + "ImageOrientationPatientDICOM": [0.996363, 0.0719648, 0.0456198, -0.051171, 0.933482, -0.354954], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(3.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-021/func/sub-01_ses-021_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 610, - -7247, - -8814, - 603, - 116, - -59, - -54, - 81 - ], + "ShimSetting": [610, -7247, -8814, 603, 116, -59, -54, 81], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_epi.json b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_epi.json index b240250c8..324ca7377 100644 --- a/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-01/ses-021/fmap/sub-01_ses-021_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.996363, - 0.0719648, - 0.0456198, - -0.051171, - 0.933482, - -0.354954 - ], + "ImageOrientationPatientDICOM": [0.996363, 0.0719648, 0.0456198, -0.051171, 0.933482, -0.354954], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(3.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-021/func/sub-01_ses-021_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 610, - -7247, - -8814, - 603, - 116, - -59, - -54, - 81 - ], + "ShimSetting": [610, -7247, -8814, 603, 116, -59, -54, 81], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, 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mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..ba4a5700e --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = e345709c-f336-42f5-912e-5126d773f20a diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..0206296f9 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 0206296f99829e3d262cbcc38b45804d44cba996 From b92b914f82b63e34b1f364f08cc9e439498c379d Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:56:15 -0400 Subject: [PATCH 162/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-03_ses-004_acq-axial_localizer.json | 81 +++ .../sub-03_ses-004_acq-axial_localizer.nii.gz | 1 + .../sub-03_ses-004_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-004_acq-coronal_localizer.nii.gz | 1 + ...sub-03_ses-004_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-004_acq-sagittal_localizer.nii.gz | 1 + sub-03/ses-004/anat/sub-03_ses-004_scout.json | 542 ++++++++++++++++++ .../ses-004/anat/sub-03_ses-004_scout.nii.gz | 1 + ...4_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-004_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...04_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...004_task-mario3_run-01_part-mag_events.tsv | 1 + ...004_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...04_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-01_part-phase_events.tsv | 1 + ...4_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-004_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...04_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...004_task-mario3_run-02_part-mag_events.tsv | 1 + ...004_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...04_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-02_part-phase_events.tsv | 1 + ...4_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-004_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...04_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...004_task-mario3_run-03_part-mag_events.tsv | 1 + ...004_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...04_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-03_part-phase_events.tsv | 1 + ...4_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-03/ses-004/sub-03_ses-004_scans.tsv | 1 + task-mario3_bold.json | 76 +++ 65 files changed, 4448 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-004/anat/sub-03_ses-004_acq-axial_localizer.json create mode 120000 sub-03/ses-004/anat/sub-03_ses-004_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-004/anat/sub-03_ses-004_acq-coronal_localizer.json create mode 120000 sub-03/ses-004/anat/sub-03_ses-004_acq-coronal_localizer.nii.gz create mode 100644 sub-03/ses-004/anat/sub-03_ses-004_acq-sagittal_localizer.json create mode 120000 sub-03/ses-004/anat/sub-03_ses-004_acq-sagittal_localizer.nii.gz create mode 100644 sub-03/ses-004/anat/sub-03_ses-004_scout.json create mode 120000 sub-03/ses-004/anat/sub-03_ses-004_scout.nii.gz create mode 100644 sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-02_part-mag_bold.json create mode 120000 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sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-03/ses-004/sub-03_ses-004_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 0206296f9..c17569dbd 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 0206296f99829e3d262cbcc38b45804d44cba996 +Subproject commit c17569dbd9d2d056fe88f725720aa97d2415d794 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git 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1.275, 0.59, 1.3725, 0.6875, 0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.08, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875], + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 237.387, + "dcmmeta_affine": [ + [-1.999088168144226, -0.047111086547374725, 0.03777925297617912, 110.12866973876953], + [-0.05544206127524376, 1.9277602434158325, -0.5297799110412598, -70.92115783691406], + [0.023935416713356972, 0.5305856466293335, 1.9281872510910034, -51.094600677490234], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From a19151860c5ce16584d28a502403fe6a6a2fcd4a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:56:47 -0400 Subject: [PATCH 163/463] fix fmap phase --- ...3_ses-004_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-004_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-004_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-004_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-004_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-004_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-03/ses-004/sub-03_ses-004_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-03/ses-004/fmap/{sub-03_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-004_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-004/fmap/{sub-03_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-004_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-004/fmap/{sub-03_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-004_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-004/fmap/{sub-03_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-004_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-004/fmap/{sub-03_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-004_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-004/fmap/{sub-03_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-004_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-004/fmap/{sub-03_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-004_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-004/fmap/{sub-03_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-004_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-03/ses-004/fmap/{sub-03_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-03_ses-004_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-03/ses-004/fmap/{sub-03_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-03_ses-004_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index e0d2abe5d..000000000 --- a/sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:01:29.472500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999544, 0.027721, 0.0119677, -0.0235555, 0.96388, -0.265293], - "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - 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- "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "135937.738000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.0534160057132, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "140215.520000", - "SliceLocation": -28.393387871562, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000000462, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "135937.656000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["140129.472500", "140130.962500", "140132.452500"], - "ContentTime": ["140215.522000", "140215.524000", "140215.527000"], - "InstanceCreationTime": ["140215.522000", "140215.524000", "140215.527000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4764.0, 4760.0, 4786.0], - "WindowWidth": [18534.0, 18534.0, 18564.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 4eee5a891..000000000 --- a/sub-03/ses-004/fmap/sub-03_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/1J/29/MD5E-s3334830--b69aec98b607ad069860cfede0269eed.nii.gz/MD5E-s3334830--b69aec98b607ad069860cfede0269eed.nii.gz \ No newline at end of file diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index a940ef3d4..000000000 --- a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:01:19.042500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999544, - 0.027721, - 0.0119677, - -0.0235555, - 0.96388, - -0.265293 - ], - "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.053416, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 619, - -7221, - -8738, - 697, - 58, - 1, - 32, - -2 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 237.387, - "WipMemBlock": "dc6c5dc6-fc0a-43aa-bd1c-4b8ae4b7d337||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 76e2f70f6..000000000 --- a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/VX/1W/MD5E-s1112215--3c8e7e4f1f5862981d3a2f2dad5fed74.nii.gz/MD5E-s1112215--3c8e7e4f1f5862981d3a2f2dad5fed74.nii.gz \ No newline at end of file diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index e0b2c86a2..000000000 --- a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:02:44.712500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999544, - 0.027721, - 0.0119677, - -0.0235555, - 0.96388, - -0.265293 - ], - "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.066979, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 619, - -7221, - -8738, - 697, - 58, - 1, - 32, - -2 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 237.387, - "WipMemBlock": "1aadc352-bc22-4393-bdd2-12e02f4d3ebd||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index bcf61ac60..000000000 --- a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/z0/WG/MD5E-s1103759--3bc1e5b50745e3b964f345b479b9d84e.nii.gz/MD5E-s1103759--3bc1e5b50745e3b964f345b479b9d84e.nii.gz \ No newline at end of file diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index c0f1d6d12..000000000 --- a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:13:33.427500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999544, - 0.027721, - 0.0119677, - -0.0235555, - 0.96388, - -0.265293 - ], - "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.066979, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 619, - -7221, - -8738, - 697, - 58, - 1, - 32, - -2 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 237.387, - "WipMemBlock": "fbba63e4-79b6-445f-9d72-87e51e51eea8||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 7b540f00e..000000000 --- a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Qm/WZ/MD5E-s1103587--1202518401eece949f2f9fba56bcbca5.nii.gz/MD5E-s1103587--1202518401eece949f2f9fba56bcbca5.nii.gz \ No newline at end of file diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 53bf8b50d..000000000 --- a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:26:48.380000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999544, - 0.027721, - 0.0119677, - -0.0235555, - 0.96388, - -0.265293 - ], - "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.066979, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 619, - -7221, - -8738, - 697, - 58, - 1, - 32, - -2 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 237.387, - "WipMemBlock": "0a200497-7f9f-4be6-b639-f7938e6d9d7f||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index bcca5f582..000000000 --- a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/PZ/6K/MD5E-s1103701--cd8894c008ce24f076c2eb43d9722aa5.nii.gz/MD5E-s1103701--cd8894c008ce24f076c2eb43d9722aa5.nii.gz \ No newline at end of file diff --git a/sub-03/ses-004/sub-03_ses-004_scans.tsv b/sub-03/ses-004/sub-03_ses-004_scans.tsv index 9b09cad4c..78a78d3fb 120000 --- a/sub-03/ses-004/sub-03_ses-004_scans.tsv +++ b/sub-03/ses-004/sub-03_ses-004_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/jz/5J/MD5E-s2667--ba8f7dcd444ff7ef7493e11292a011aa.tsv/MD5E-s2667--ba8f7dcd444ff7ef7493e11292a011aa.tsv \ No newline at end of file +../../.git/annex/objects/Xp/78/MD5E-s2066--11ab7dcfb77fcc8841d2edf753514863.tsv/MD5E-s2066--11ab7dcfb77fcc8841d2edf753514863.tsv \ No newline at end of file From 964dadcad00f4826c9696507b814e263dfff87f6 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:56:55 -0400 Subject: [PATCH 164/463] fix complex event files --- ...g_events.tsv => sub-03_ses-004_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-03_ses-004_task-mario3_run-02_events.tsv} | 0 .../func/sub-03_ses-004_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-03_ses-004_task-mario3_run-03_events.tsv} | 0 .../func/sub-03_ses-004_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-03_ses-004_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-03/ses-004/func/{sub-03_ses-004_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-004_task-mario3_run-01_events.tsv} (100%) rename sub-03/ses-004/func/{sub-03_ses-004_task-mario3_run-01_part-phase_events.tsv => sub-03_ses-004_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-02_part-phase_events.tsv rename sub-03/ses-004/func/{sub-03_ses-004_task-mario3_run-02_part-mag_events.tsv => sub-03_ses-004_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-02_events.tsv similarity index 100% rename from sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-01_part-phase_events.tsv rename to sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-02_events.tsv diff --git a/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-02_part-phase_events.tsv b/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-02_part-mag_events.tsv b/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_events.tsv similarity index 100% rename from sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-02_part-mag_events.tsv rename to sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_events.tsv diff --git a/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_part-mag_events.tsv b/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_part-phase_events.tsv b/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 95c237cd9df12cc63ef26d1da88132787759966c Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:57:27 -0400 Subject: [PATCH 165/463] fill IntendedFor --- ...3_ses-004_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...3_ses-004_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...3_ses-004_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...3_ses-004_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_epi.json index 011afc472..176e22e17 100644 --- a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999544, - 0.027721, - 0.0119677, - -0.0235555, - 0.96388, - -0.265293 - ], + "ImageOrientationPatientDICOM": [0.999544, 0.027721, 0.0119677, -0.0235555, 0.96388, -0.265293], "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-03_ses-004_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-004/func/sub-03_ses-004_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-004/func/sub-03_ses-004_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 619, - -7221, - -8738, - 697, - 58, - 1, - 32, - -2 - ], + "ShimSetting": [619, -7221, -8738, 697, 58, 1, 32, -2], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_epi.json b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_epi.json index ac44a0a14..56e20f1bd 100644 --- a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999544, - 0.027721, - 0.0119677, - -0.0235555, - 0.96388, - -0.265293 - ], + "ImageOrientationPatientDICOM": [0.999544, 0.027721, 0.0119677, -0.0235555, 0.96388, -0.265293], "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-03_ses-004_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 619, - -7221, - -8738, - 697, - 58, - 1, - 32, - -2 - ], + "ShimSetting": [619, -7221, -8738, 697, 58, 1, 32, -2], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_epi.json b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_epi.json index 5c1e0016e..101da8c58 100644 --- a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999544, - 0.027721, - 0.0119677, - -0.0235555, - 0.96388, - -0.265293 - ], + "ImageOrientationPatientDICOM": [0.999544, 0.027721, 0.0119677, -0.0235555, 0.96388, -0.265293], "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-03_ses-004_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 619, - -7221, - -8738, - 697, - 58, - 1, - 32, - -2 - ], + "ShimSetting": [619, -7221, -8738, 697, 58, 1, 32, -2], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_epi.json b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_epi.json index 74a2adf0a..783f8dbd1 100644 --- a/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-03/ses-004/fmap/sub-03_ses-004_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999544, - 0.027721, - 0.0119677, - -0.0235555, - 0.96388, - -0.265293 - ], + "ImageOrientationPatientDICOM": [0.999544, 0.027721, 0.0119677, -0.0235555, 0.96388, -0.265293], "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-03_ses-004_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 619, - -7221, - -8738, - 697, - 58, - 1, - 32, - -2 - ], + "ShimSetting": [619, -7221, -8738, 697, 58, 1, 32, -2], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 636c0be50b38ce33c2a5dacd963b1ffcc4b6f109 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:58:23 -0400 Subject: [PATCH 166/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..0571bc2fc --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = e321787f-557b-4e27-b060-1801aac2d6fa diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..718da6ac2 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 718da6ac2b81afb8bda118589a7f8b6f257407e5 From 8cfaee22621b1147e3fabfb52723e98ab89ce0e3 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:58:38 -0400 Subject: [PATCH 167/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-03_ses-010_acq-axial_localizer.json | 81 +++ .../sub-03_ses-010_acq-axial_localizer.nii.gz | 1 + ...3_ses-010_acq-axial_localizer__dup-01.json | 81 +++ ...ses-010_acq-axial_localizer__dup-01.nii.gz | 1 + .../sub-03_ses-010_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-010_acq-coronal_localizer.nii.gz | 1 + ...ses-010_acq-coronal_localizer__dup-01.json | 81 +++ ...s-010_acq-coronal_localizer__dup-01.nii.gz | 1 + ...sub-03_ses-010_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-010_acq-sagittal_localizer.nii.gz | 1 + ...es-010_acq-sagittal_localizer__dup-01.json | 86 +++ ...-010_acq-sagittal_localizer__dup-01.nii.gz | 1 + sub-03/ses-010/anat/sub-03_ses-010_scout.json | 542 ++++++++++++++++++ .../ses-010/anat/sub-03_ses-010_scout.nii.gz | 1 + ...0_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ...-010_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...10_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...k-mario3_run-01_part-mag_bold__dup-01.json | 172 ++++++ ...mario3_run-01_part-mag_bold__dup-01.nii.gz | 1 + ...010_task-mario3_run-01_part-mag_events.tsv | 1 + ...010_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...0_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...10_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...mario3_run-01_part-phase_bold__dup-01.json | 178 ++++++ ...rio3_run-01_part-phase_bold__dup-01.nii.gz | 1 + ...0_task-mario3_run-01_part-phase_events.tsv | 1 + ...0_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-mario3_run-01_sbref__part-mag_dup-01.json | 150 +++++ ...ario3_run-01_sbref__part-mag_dup-01.nii.gz | 1 + ...ario3_run-01_sbref__part-phase_dup-01.json | 153 +++++ ...io3_run-01_sbref__part-phase_dup-01.nii.gz | 1 + sub-03/ses-010/sub-03_ses-010_scans.tsv | 1 + task-mario3_bold.json | 81 +++ 55 files changed, 3740 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-010/anat/sub-03_ses-010_acq-axial_localizer.json create mode 120000 sub-03/ses-010/anat/sub-03_ses-010_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-010/anat/sub-03_ses-010_acq-axial_localizer__dup-01.json create mode 120000 sub-03/ses-010/anat/sub-03_ses-010_acq-axial_localizer__dup-01.nii.gz create mode 100644 sub-03/ses-010/anat/sub-03_ses-010_acq-coronal_localizer.json create mode 120000 sub-03/ses-010/anat/sub-03_ses-010_acq-coronal_localizer.nii.gz create mode 100644 sub-03/ses-010/anat/sub-03_ses-010_acq-coronal_localizer__dup-01.json create mode 120000 sub-03/ses-010/anat/sub-03_ses-010_acq-coronal_localizer__dup-01.nii.gz create mode 100644 sub-03/ses-010/anat/sub-03_ses-010_acq-sagittal_localizer.json create mode 120000 sub-03/ses-010/anat/sub-03_ses-010_acq-sagittal_localizer.nii.gz create mode 100644 sub-03/ses-010/anat/sub-03_ses-010_acq-sagittal_localizer__dup-01.json create mode 120000 sub-03/ses-010/anat/sub-03_ses-010_acq-sagittal_localizer__dup-01.nii.gz create mode 100644 sub-03/ses-010/anat/sub-03_ses-010_scout.json create mode 120000 sub-03/ses-010/anat/sub-03_ses-010_scout.nii.gz create mode 100644 sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-mag_bold.nii.gz create mode 100644 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-mag_bold__dup-01.json create mode 120000 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-mag_bold__dup-01.nii.gz create mode 120000 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-phase_bold.nii.gz create mode 100644 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-phase_bold__dup-01.json create mode 120000 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-phase_bold__dup-01.nii.gz create mode 120000 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_sbref__part-mag_dup-01.json create mode 120000 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_sbref__part-mag_dup-01.nii.gz create mode 100644 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_sbref__part-phase_dup-01.json create mode 120000 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_sbref__part-phase_dup-01.nii.gz create mode 120000 sub-03/ses-010/sub-03_ses-010_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 718da6ac2..70c6968d4 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 718da6ac2b81afb8bda118589a7f8b6f257407e5 +Subproject commit 70c6968d4b1abc5cc1e0bf02db5553ccda915710 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-03/ses-010/anat/sub-03_ses-010_acq-axial_localizer.json b/sub-03/ses-010/anat/sub-03_ses-010_acq-axial_localizer.json new file mode 100644 index 000000000..b856a49b8 --- /dev/null +++ b/sub-03/ses-010/anat/sub-03_ses-010_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "14:11:33.070000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + 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-0,0 +1 @@ +../../../.git/annex/objects/xw/8k/MD5E-s165126--64917e62dfd296c5612b67d6eb2a8538.nii.gz/MD5E-s165126--64917e62dfd296c5612b67d6eb2a8538.nii.gz \ No newline at end of file diff --git a/sub-03/ses-010/anat/sub-03_ses-010_acq-axial_localizer__dup-01.json b/sub-03/ses-010/anat/sub-03_ses-010_acq-axial_localizer__dup-01.json new file mode 100644 index 000000000..9672e1216 --- /dev/null +++ b/sub-03/ses-010/anat/sub-03_ses-010_acq-axial_localizer__dup-01.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "14:10:33.040000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + 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a/sub-03/ses-010/anat/sub-03_ses-010_acq-coronal_localizer__dup-01.json b/sub-03/ses-010/anat/sub-03_ses-010_acq-coronal_localizer__dup-01.json new file mode 100644 index 000000000..10bdb5de7 --- /dev/null +++ b/sub-03/ses-010/anat/sub-03_ses-010_acq-coronal_localizer__dup-01.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "14:10:40.030000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + 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"CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999728, 0.0156518, 0.0173084, -0.0104695, 0.963707, -0.266758], + "ImageOrientationText": "Tra>Cor(-15.5)>Sag(1.2)", + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "func_task-mario3_run-01", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0655533, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "SeriesDescription": "func_task-mario3_run-01", + "ShimSetting": [620, -7214, -8768, 669, 70, 19, 6, 0], + "SliceThickness": 2, + "SliceTiming": [0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.08, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875, 0, 0.785, 0.1, 0.8825, 0.1975, 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[0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_shape": [104, 104, 60, 407], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 9b8140a6233802f6e15aa790140ac336483f8d14 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:58:53 -0400 Subject: [PATCH 168/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..01b78949f --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = a221ad07-1b18-4af6-b2c7-ceaf5f5c7559 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..524a17184 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 524a171841aa5915e62dff159bb13b0ddd997adc From 98483a79ec0123a24e597fbd872142a9bd4cba40 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:59:05 -0400 Subject: [PATCH 169/463] fix fmap phase --- ...3_ses-010_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-010_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-010_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-010_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-010_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - sub-03/ses-010/sub-03_ses-010_scans.tsv | 2 +- 17 files changed, 1 insertion(+), 638 deletions(-) rename sub-03/ses-010/fmap/{sub-03_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-010_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-010/fmap/{sub-03_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-010_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-010/fmap/{sub-03_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-010_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-010/fmap/{sub-03_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-010_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-010/fmap/{sub-03_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-010_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-010/fmap/{sub-03_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-010_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-010/fmap/{sub-03_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-010_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-010/fmap/{sub-03_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-010_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz diff --git a/sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 80cba91ea..000000000 --- a/sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:12:32.267500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999728, 0.0156518, 0.0173084, -0.0104695, 0.963707, -0.266758], - "ImageOrientationText": 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"HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.052279, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 9, - "ShimSetting": [620, -7214, -8768, 669, 70, 19, 6, 0], - "SliceThickness": 2, - "SliceTiming": [0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 238.619, - "WipMemBlock": "d56fda38-3d64-4be0-bb16-3c19cab1c8f0||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9994553327560425, -0.020938975736498833, 0.04171093553304672, 109.0552978515625], - [-0.03130367770791054, 1.9274135828018188, -0.5330074429512024, -71.73737335205078], - [0.03461679443717003, 0.5335151553153992, 1.9272165298461914, -56.58720779418945], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99972768259517, 0.01565183839575, 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0.05227902975972, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 9, - "SeriesTime": "141318.141000", - "SliceLocation": -33.135220435981, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000634556, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "140249.506000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["141232.267500", "141233.757500", "141235.247500"], - "ContentTime": ["141318.144000", "141318.146000", "141318.149000"], - "InstanceCreationTime": ["141318.144000", "141318.146000", "141318.149000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4796.0, 4792.0, 4794.0], - "WindowWidth": [18612.0, 18618.0, 18612.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index e5129d020..000000000 --- a/sub-03/ses-010/fmap/sub-03_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/5z/G0/MD5E-s3334999--3c866d834b09ea442ad65a9a7c58950a.nii.gz/MD5E-s3334999--3c866d834b09ea442ad65a9a7c58950a.nii.gz \ No newline at end of file diff --git a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 767e1aa5f..000000000 --- a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:12:21.837500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999728, - 0.0156518, - 0.0173084, - -0.0104695, - 0.963707, - -0.266758 - ], - "ImageOrientationText": "Tra>Cor(-15.5)>Sag(1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.052279, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 7, - "ShimSetting": [ - 620, - -7214, - -8768, - 669, - 70, - 19, - 6, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 238.619, - "WipMemBlock": "d56fda38-3d64-4be0-bb16-3c19cab1c8f0||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 7220cb3d6..000000000 --- a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/mj/xf/MD5E-s1112162--53a5979f6368d35f29b982b23e463a09.nii.gz/MD5E-s1112162--53a5979f6368d35f29b982b23e463a09.nii.gz \ No newline at end of file diff --git a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 95511d3a5..000000000 --- a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:14:25.282500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999728, - 0.0156518, - 0.0173084, - -0.0104695, - 0.963707, - -0.266758 - ], - "ImageOrientationText": "Tra>Cor(-15.5)>Sag(1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0655533, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 10, - "ShimSetting": [ - 620, - -7214, - -8768, - 669, - 70, - 19, - 6, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 238.619, - "WipMemBlock": "b867e765-43f6-4378-88be-68eadd295962||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index f4ca73b91..000000000 --- a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/1p/2q/MD5E-s1103648--159865ba1e51e9704be9e61b7000b2fa.nii.gz/MD5E-s1103648--159865ba1e51e9704be9e61b7000b2fa.nii.gz \ No newline at end of file diff --git a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index b58a46289..000000000 --- a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:17:23.972500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999728, - 0.0156518, - 0.0173084, - -0.0104695, - 0.963707, - -0.266758 - ], - "ImageOrientationText": "Tra>Cor(-15.5)>Sag(1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0655533, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 13, - "ShimSetting": [ - 620, - -7214, - -8768, - 669, - 70, - 19, - 6, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 238.619, - "WipMemBlock": "62a0a6ea-137b-4d31-8a44-3aac625499c2||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 0bd2c2ec8..000000000 --- a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/k1/Fm/MD5E-s1103777--71e9fde2bb1baedb45d93456428389e3.nii.gz/MD5E-s1103777--71e9fde2bb1baedb45d93456428389e3.nii.gz \ No newline at end of file diff --git a/sub-03/ses-010/sub-03_ses-010_scans.tsv b/sub-03/ses-010/sub-03_ses-010_scans.tsv index 4c8b6ceab..d40b40396 120000 --- a/sub-03/ses-010/sub-03_ses-010_scans.tsv +++ b/sub-03/ses-010/sub-03_ses-010_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/gM/PP/MD5E-s2370--dc5fe0446ae51272240e4c46d62f070c.tsv/MD5E-s2370--dc5fe0446ae51272240e4c46d62f070c.tsv \ No newline at end of file +../../.git/annex/objects/57/z8/MD5E-s1887--b9b62c0f8b059facd222afcb9b108e30.tsv/MD5E-s1887--b9b62c0f8b059facd222afcb9b108e30.tsv \ No newline at end of file From 628c1d6963541aef8667aa549d3f2f7f0b1659ad Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 15:59:11 -0400 Subject: [PATCH 170/463] fix complex event files --- ...g_events.tsv => sub-03_ses-010_task-mario3_run-01_events.tsv} | 0 .../func/sub-03_ses-010_task-mario3_run-01_part-phase_events.tsv | 1 - 2 files changed, 1 deletion(-) rename sub-03/ses-010/func/{sub-03_ses-010_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-010_task-mario3_run-01_events.tsv} (100%) delete mode 120000 sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-phase_events.tsv diff --git a/sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-010/func/sub-03_ses-010_task-mario3_run-01_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 2eec1a9125d7210dffba0ec78812ee356ceb3adb Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:00:31 -0400 Subject: [PATCH 171/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..f62fabf4d --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = f38f0f52-3939-4ef0-9774-70a1ef566891 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..f115ad775 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit f115ad7752b88ff03b5c6ae948e784c6f5ae65f2 From db82d050b18c6fd9d96e2a17cda5430fdad31b68 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:00:49 -0400 Subject: [PATCH 172/463] fill IntendedFor --- ...3_ses-010_acq-sbref_dir-AP_run-01_epi.json | 88 ++----------------- ...3_ses-010_acq-sbref_dir-PA_run-02_epi.json | 88 ++----------------- 2 files changed, 14 insertions(+), 162 deletions(-) diff --git a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_epi.json index 9d5819755..0442d5e89 100644 --- a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999728, - 0.0156518, - 0.0173084, - -0.0104695, - 0.963707, - -0.266758 - ], + "ImageOrientationPatientDICOM": [0.999728, 0.0156518, 0.0173084, -0.0104695, 0.963707, -0.266758], "ImageOrientationText": "Tra>Cor(-15.5)>Sag(1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-03_ses-010_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 7, - "ShimSetting": [ - 620, - -7214, - -8768, - 669, - 70, - 19, - 6, - 0 - ], + "ShimSetting": [620, -7214, -8768, 669, 70, 19, 6, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_epi.json b/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_epi.json index 058ed6575..16f0270d1 100644 --- a/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-03/ses-010/fmap/sub-03_ses-010_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999728, - 0.0156518, - 0.0173084, - -0.0104695, - 0.963707, - -0.266758 - ], + "ImageOrientationPatientDICOM": [0.999728, 0.0156518, 0.0173084, -0.0104695, 0.963707, -0.266758], "ImageOrientationText": "Tra>Cor(-15.5)>Sag(1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-03_ses-010_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 13, - "ShimSetting": [ - 620, - -7214, - -8768, - 669, - 70, - 19, - 6, - 0 - ], + "ShimSetting": [620, -7214, -8768, 669, 70, 19, 6, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.02, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From cb253a1b4a7d057991b32b9bf06bcd2fd7fc8fc6 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:00:56 -0400 Subject: [PATCH 173/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-012_acq-axial_localizer.json | 81 +++ .../sub-02_ses-012_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-012_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-012_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-012_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-012_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-012/anat/sub-02_ses-012_scout.json | 542 ++++++++++++++++++ .../ses-012/anat/sub-02_ses-012_scout.nii.gz | 1 + ...2_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-012_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...12_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...012_task-mario3_run-01_part-mag_events.tsv | 1 + ...012_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...12_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-01_part-phase_events.tsv | 1 + ...2_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-012_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...12_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...012_task-mario3_run-02_part-mag_events.tsv | 1 + ...012_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...12_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-02_part-phase_events.tsv | 1 + ...2_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-012_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...12_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...012_task-mario3_run-03_part-mag_events.tsv | 1 + ...012_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...12_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-03_part-phase_events.tsv | 1 + ...2_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-012_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...12_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...012_task-mario3_run-04_part-mag_events.tsv | 1 + ...012_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...12_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-04_part-phase_events.tsv | 1 + ...2_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-02/ses-012/sub-02_ses-012_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5409 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-012/anat/sub-02_ses-012_acq-axial_localizer.json create mode 120000 sub-02/ses-012/anat/sub-02_ses-012_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-012/anat/sub-02_ses-012_acq-coronal_localizer.json create mode 120000 sub-02/ses-012/anat/sub-02_ses-012_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-012/anat/sub-02_ses-012_acq-sagittal_localizer.json create mode 120000 sub-02/ses-012/anat/sub-02_ses-012_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-012/anat/sub-02_ses-012_scout.json create mode 120000 sub-02/ses-012/anat/sub-02_ses-012_scout.nii.gz create mode 100644 sub-02/ses-012/fmap/sub-02_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-012/fmap/sub-02_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-012/fmap/sub-02_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-012/fmap/sub-02_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 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f115ad7752b88ff03b5c6ae948e784c6f5ae65f2 +Subproject commit 80edb7480e2443dee1591bd70a6259073adeb8b1 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..83ada7a9d --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 51 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-012/anat/sub-02_ses-012_acq-axial_localizer.json b/sub-02/ses-012/anat/sub-02_ses-012_acq-axial_localizer.json new file mode 100644 index 000000000..92fed989c --- /dev/null +++ b/sub-02/ses-012/anat/sub-02_ses-012_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:36:23.195000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 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newline at end of file diff --git a/sub-02/ses-012/anat/sub-02_ses-012_acq-coronal_localizer.nii.gz b/sub-02/ses-012/anat/sub-02_ses-012_acq-coronal_localizer.nii.gz new file mode 120000 index 000000000..60b6cbed7 --- /dev/null +++ b/sub-02/ses-012/anat/sub-02_ses-012_acq-coronal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/gm/Vk/MD5E-s203909--a98b42c69a75cdf44806bea4c9c9a2f4.nii.gz/MD5E-s203909--a98b42c69a75cdf44806bea4c9c9a2f4.nii.gz \ No newline at end of file diff --git a/sub-02/ses-012/anat/sub-02_ses-012_acq-sagittal_localizer.json b/sub-02/ses-012/anat/sub-02_ses-012_acq-sagittal_localizer.json new file mode 100644 index 000000000..cfa5836eb --- /dev/null +++ b/sub-02/ses-012/anat/sub-02_ses-012_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:36:16.205000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": 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-210, + -56, + 39 + ], + "SliceThickness": 2, + "SliceTiming": [ + 0, + 0.0975, + 0.1975, + 0.295, + 0.3925, + 0.49, + 0.5875, + 0.6875, + 0.785, + 0.8825, + 0.98, + 1.0775, + 1.1775, + 1.275, + 1.3725, + 1.47, + 1.5675, + 1.6675, + 1.765, + 1.8625, + 1.96, + 2.0575, + 2.155, + 2.255, + 2.3525, + 2.45, + 2.5475, + 2.645, + 2.745, + 2.8425, + 2.94, + 3.0375, + 3.135, + 3.235, + 3.3325, + 3.43, + 3.5275, + 3.625, + 3.725, + 3.8225, + 3.92, + 4.0175, + 4.115, + 4.215, + 4.3125, + 4.41, + 4.5075, + 4.605, + 4.705, + 4.8025, + 4.9, + 4.9975, + 5.095, + 5.195, + 5.2925, + 5.39, + 5.4875, + 5.585, + 5.685, + 5.7825 + ], + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 307.829, + "WipMemBlock": "c0944c4f-202b-4a7b-ba22-f5bf99e20e5d||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-04_part-phase_sbref.nii.gz b/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-04_part-phase_sbref.nii.gz new file mode 120000 index 000000000..497c073e9 --- /dev/null +++ b/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-04_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/vw/wW/MD5E-s1103397--3a2f1ad502b8ab161afa04ee087e57c7.nii.gz/MD5E-s1103397--3a2f1ad502b8ab161afa04ee087e57c7.nii.gz \ No newline at end of file diff --git a/sub-02/ses-012/sub-02_ses-012_scans.tsv b/sub-02/ses-012/sub-02_ses-012_scans.tsv new file mode 120000 index 000000000..6cb26d5f7 --- /dev/null +++ b/sub-02/ses-012/sub-02_ses-012_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/WP/qw/MD5E-s3289--6e9c5a110ad73cc95e1aa468914eb593.tsv/MD5E-s3289--6e9c5a110ad73cc95e1aa468914eb593.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..2c82832c8 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.998066, -0.00417824, 0.0620243, 0.0378185, 0.832679, -0.552464], + "ImageOrientationText": "Tra>Cor(-33.7)>Sag(2.8)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0745806, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [620, -7193, -8856, 229, -20, -210, -56, 39], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 307.829, + "dcmmeta_affine": [ + [-1.9961317777633667, 0.07563691586256027, 0.09867603331804276, 100.79991912841797], + [0.00835647713392973, 1.6653573513031006, -1.1074813604354858, -46.39983367919922], + [0.12404866516590118, 1.1049270629882812, 1.6624524593353271, -88.29158782958984], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 5c3d1d06de7e54b24203f43be4f8babe612c400f Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:01:05 -0400 Subject: [PATCH 174/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..8ec0a3bf6 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = baf4934d-6885-4c32-b297-416ab58657ad diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..6633341ca --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 6633341cac1b0346290e362f2502ac3b5ca8afb2 From 0fec23cded6d3a4698abbac842d7bd0e7792b3a6 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:01:20 -0400 Subject: [PATCH 175/463] fix fmap phase --- ...2_ses-012_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-012_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-012_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-012_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-012_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-012_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-012_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-012_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-012_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-012_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-012_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-012_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-02/ses-012/sub-02_ses-012_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-02/ses-012/fmap/{sub-02_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-012_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-012/fmap/{sub-02_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-012_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-012/fmap/sub-02_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-012/fmap/sub-02_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-012/fmap/{sub-02_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-012_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-012/fmap/{sub-02_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-012_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-012/fmap/{sub-02_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-012_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-012/fmap/{sub-02_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-012_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-012/fmap/{sub-02_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-012_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-012/fmap/{sub-02_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-012_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-012/fmap/{sub-02_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-012_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-012/fmap/{sub-02_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-012_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-02/ses-012/fmap/{sub-02_ses-012_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-02_ses-012_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-02/ses-012/fmap/{sub-02_ses-012_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-02_ses-012_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-012/fmap/sub-02_ses-012_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-012/fmap/sub-02_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-012/fmap/sub-02_ses-012_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-012/fmap/sub-02_ses-012_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-012/fmap/sub-02_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-012/fmap/sub-02_ses-012_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-012/fmap/sub-02_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index d309f7642..000000000 --- a/sub-02/ses-012/fmap/sub-02_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:38:9.627500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.998066, -0.00417824, 0.0620243, 0.0378185, 0.832679, -0.552464], - "ImageOrientationText": "Tra>Cor(-33.7)>Sag(2.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": 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0.05947834302258, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "113859.244000", - "SliceLocation": -42.723539239536, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000053286, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "113329.449000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["113809.627500", "113811.117500", "113812.607500"], - "ContentTime": ["113859.246000", "113859.249000", "113859.252000"], - "InstanceCreationTime": ["113859.246000", "113859.249000", "113859.252000"], - "InstanceNumber": [1, 2, 3], - 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sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index fa200f38a..000000000 --- a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:37:59.197500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of 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"MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0594783, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 620, - -7193, - -8856, - 229, - -20, - -210, - -56, - 39 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, 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b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 9e864a9c5..000000000 --- a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Kj/kg/MD5E-s1112257--bb7ba6e95559e634470b6a8e719ba4fa.nii.gz/MD5E-s1112257--bb7ba6e95559e634470b6a8e719ba4fa.nii.gz \ No newline at end of file diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 47e586d0f..000000000 --- a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:38:30.895000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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"PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0745806, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 620, - -7193, - -8856, - 229, - -20, - -210, - -56, - 39 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 307.829, - "WipMemBlock": "bc9a262d-717c-412b-8a90-ef2ae8f5f507||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index a7415804c..000000000 --- a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/V3/gZ/MD5E-s1103357--4ee7c811c18821801f0ba437b62fe4fd.nii.gz/MD5E-s1103357--4ee7c811c18821801f0ba437b62fe4fd.nii.gz \ No newline at end of file diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 47ed862e8..000000000 --- a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:47:33.697500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998066, - -0.00417824, - 0.0620243, - 0.0378185, - 0.832679, - -0.552464 - ], - "ImageOrientationText": "Tra>Cor(-33.7)>Sag(2.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0745806, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 620, - -7193, - -8856, - 229, - -20, - -210, - -56, - 39 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 307.829, - "WipMemBlock": "84c640a9-e5f7-4f42-96c5-6abd99b973ef||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index ca7aa8d52..000000000 --- a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/m7/k9/MD5E-s1103393--7897429e6b0ca2234300990736cf1398.nii.gz/MD5E-s1103393--7897429e6b0ca2234300990736cf1398.nii.gz \ No newline at end of file diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 6ee73a9bb..000000000 --- a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:57:16.985000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998066, - -0.00417824, - 0.0620243, - 0.0378185, - 0.832679, - -0.552464 - ], - "ImageOrientationText": "Tra>Cor(-33.7)>Sag(2.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0745806, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 620, - -7193, - -8856, - 229, - -20, - -210, - -56, - 39 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 307.829, - "WipMemBlock": "52441293-e7d9-40b2-a427-a5763240b8ea||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 261322f3a..000000000 --- a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/PX/j4/MD5E-s1103340--3481430051f6be9ba123a802d0be6d19.nii.gz/MD5E-s1103340--3481430051f6be9ba123a802d0be6d19.nii.gz \ No newline at end of file diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index ec6db849d..000000000 --- a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "12:06:49.122500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998066, - -0.00417824, - 0.0620243, - 0.0378185, - 0.832679, - -0.552464 - ], - "ImageOrientationText": "Tra>Cor(-33.7)>Sag(2.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0745806, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 620, - -7193, - -8856, - 229, - -20, - -210, - -56, - 39 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 307.829, - "WipMemBlock": "c0944c4f-202b-4a7b-ba22-f5bf99e20e5d||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 497c073e9..000000000 --- a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/vw/wW/MD5E-s1103397--3a2f1ad502b8ab161afa04ee087e57c7.nii.gz/MD5E-s1103397--3a2f1ad502b8ab161afa04ee087e57c7.nii.gz \ No newline at end of file diff --git a/sub-02/ses-012/sub-02_ses-012_scans.tsv b/sub-02/ses-012/sub-02_ses-012_scans.tsv index 6cb26d5f7..50826b34d 120000 --- a/sub-02/ses-012/sub-02_ses-012_scans.tsv +++ b/sub-02/ses-012/sub-02_ses-012_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/WP/qw/MD5E-s3289--6e9c5a110ad73cc95e1aa468914eb593.tsv/MD5E-s3289--6e9c5a110ad73cc95e1aa468914eb593.tsv \ No newline at end of file +../../.git/annex/objects/wF/5g/MD5E-s2567--73e6368259d23123510bbb8256a7fb95.tsv/MD5E-s2567--73e6368259d23123510bbb8256a7fb95.tsv \ No newline at end of file From 41458a39f979b86ee638aee2214f472e3d30ca25 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:01:26 -0400 Subject: [PATCH 176/463] fix complex event files --- ...g_events.tsv => sub-02_ses-012_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-02_ses-012_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-02_ses-012_task-mario3_run-03_events.tsv} | 0 .../func/sub-02_ses-012_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-02_ses-012_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-02_ses-012_task-mario3_run-04_events.tsv} | 0 .../func/sub-02_ses-012_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-02_ses-012_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-02/ses-012/func/{sub-02_ses-012_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-012_task-mario3_run-01_events.tsv} (100%) rename sub-02/ses-012/func/{sub-02_ses-012_task-mario3_run-01_part-phase_events.tsv => sub-02_ses-012_task-mario3_run-02_events.tsv} (100%) rename sub-02/ses-012/func/{sub-02_ses-012_task-mario3_run-02_part-mag_events.tsv => sub-02_ses-012_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_part-phase_events.tsv rename sub-02/ses-012/func/{sub-02_ses-012_task-mario3_run-02_part-phase_events.tsv => sub-02_ses-012_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-02_events.tsv similarity index 100% rename from sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-01_part-phase_events.tsv rename to sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-02_events.tsv diff --git a/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-02_part-mag_events.tsv b/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_events.tsv similarity index 100% rename from sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-02_part-mag_events.tsv rename to sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_events.tsv diff --git a/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_part-mag_events.tsv b/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-02_part-phase_events.tsv b/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-04_events.tsv similarity index 100% rename from sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-02_part-phase_events.tsv rename to sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-04_events.tsv diff --git a/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-04_part-mag_events.tsv b/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-04_part-phase_events.tsv b/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-012/func/sub-02_ses-012_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 9212b1477cdd8873ed1eb220946276f1c235936e Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:02:17 -0400 Subject: [PATCH 177/463] fill IntendedFor --- ...2_ses-012_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...2_ses-012_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...2_ses-012_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...2_ses-012_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...2_ses-012_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_epi.json index a27c90503..daea2c106 100644 --- a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998066, - -0.00417824, - 0.0620243, - 0.0378185, - 0.832679, - -0.552464 - ], + "ImageOrientationPatientDICOM": [0.998066, -0.00417824, 0.0620243, 0.0378185, 0.832679, -0.552464], "ImageOrientationText": "Tra>Cor(-33.7)>Sag(2.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-012/func/sub-02_ses-012_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-012/func/sub-02_ses-012_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-012/func/sub-02_ses-012_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-012/func/sub-02_ses-012_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 620, - -7193, - -8856, - 229, - -20, - -210, - -56, - 39 - ], + "ShimSetting": [620, -7193, -8856, 229, -20, -210, -56, 39], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_epi.json b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_epi.json index 8a589d705..ce1e8220e 100644 --- a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998066, - -0.00417824, - 0.0620243, - 0.0378185, - 0.832679, - -0.552464 - ], + "ImageOrientationPatientDICOM": [0.998066, -0.00417824, 0.0620243, 0.0378185, 0.832679, -0.552464], "ImageOrientationText": "Tra>Cor(-33.7)>Sag(2.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-012/func/sub-02_ses-012_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 620, - -7193, - -8856, - 229, - -20, - -210, - -56, - 39 - ], + "ShimSetting": [620, -7193, -8856, 229, -20, -210, -56, 39], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_epi.json b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_epi.json index 745ce36e6..3d0723c92 100644 --- a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998066, - -0.00417824, - 0.0620243, - 0.0378185, - 0.832679, - -0.552464 - ], + "ImageOrientationPatientDICOM": [0.998066, -0.00417824, 0.0620243, 0.0378185, 0.832679, -0.552464], "ImageOrientationText": "Tra>Cor(-33.7)>Sag(2.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-012/func/sub-02_ses-012_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 620, - -7193, - -8856, - 229, - -20, - -210, - -56, - 39 - ], + "ShimSetting": [620, -7193, -8856, 229, -20, -210, -56, 39], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_epi.json b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_epi.json index 547baf6f9..69c081b9f 100644 --- a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998066, - -0.00417824, - 0.0620243, - 0.0378185, - 0.832679, - -0.552464 - ], + "ImageOrientationPatientDICOM": [0.998066, -0.00417824, 0.0620243, 0.0378185, 0.832679, -0.552464], "ImageOrientationText": "Tra>Cor(-33.7)>Sag(2.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-012/func/sub-02_ses-012_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 620, - -7193, - -8856, - 229, - -20, - -210, - -56, - 39 - ], + "ShimSetting": [620, -7193, -8856, 229, -20, -210, -56, 39], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_epi.json b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_epi.json index 256f36ae4..be83a5b44 100644 --- a/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-02/ses-012/fmap/sub-02_ses-012_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998066, - -0.00417824, - 0.0620243, - 0.0378185, - 0.832679, - -0.552464 - ], + "ImageOrientationPatientDICOM": [0.998066, -0.00417824, 0.0620243, 0.0378185, 0.832679, -0.552464], "ImageOrientationText": "Tra>Cor(-33.7)>Sag(2.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-012/func/sub-02_ses-012_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 620, - -7193, - -8856, - 229, - -20, - -210, - -56, - 39 - ], + "ShimSetting": [620, -7193, -8856, 229, -20, -210, -56, 39], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From f45f84fd8df20638ada1e3f75ce8ecbf422bed3d Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:04:25 -0400 Subject: [PATCH 178/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..05a03aec9 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 8124ac6a-1a0c-4404-a9f2-2a99846e8a64 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..9a21d6259 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 9a21d62591e52b2da8324f450e3bc514172c0c1c From ba58251082057c334935298c5f1b25b410a09d1c Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:04:47 -0400 Subject: [PATCH 179/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-010_acq-axial_localizer.json | 81 +++ .../sub-02_ses-010_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-010_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-010_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-010_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-010_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-010/anat/sub-02_ses-010_scout.json | 542 ++++++++++++++++++ .../ses-010/anat/sub-02_ses-010_scout.nii.gz | 1 + ...0_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-010_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...10_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...010_task-mario3_run-01_part-mag_events.tsv | 1 + ...010_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...0_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...10_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...0_task-mario3_run-01_part-phase_events.tsv | 1 + ...0_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-010_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...10_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...010_task-mario3_run-02_part-mag_events.tsv | 1 + ...010_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...0_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...10_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...0_task-mario3_run-02_part-phase_events.tsv | 1 + ...0_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-010_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...10_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...010_task-mario3_run-03_part-mag_events.tsv | 1 + ...010_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...0_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...10_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...0_task-mario3_run-03_part-phase_events.tsv | 1 + ...0_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-02/ses-010/sub-02_ses-010_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-010/anat/sub-02_ses-010_acq-axial_localizer.json create mode 120000 sub-02/ses-010/anat/sub-02_ses-010_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-010/anat/sub-02_ses-010_acq-coronal_localizer.json create mode 120000 sub-02/ses-010/anat/sub-02_ses-010_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-010/anat/sub-02_ses-010_acq-sagittal_localizer.json create mode 120000 sub-02/ses-010/anat/sub-02_ses-010_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-010/anat/sub-02_ses-010_scout.json create mode 120000 sub-02/ses-010/anat/sub-02_ses-010_scout.nii.gz create mode 100644 sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-02/ses-010/sub-02_ses-010_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 9a21d6259..25864cbcf 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 9a21d62591e52b2da8324f450e3bc514172c0c1c +Subproject commit 25864cbcf5cb935fbe1a76009cb535c77e702722 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..24e351d98 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 41 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-010/anat/sub-02_ses-010_acq-axial_localizer.json b/sub-02/ses-010/anat/sub-02_ses-010_acq-axial_localizer.json new file mode 100644 index 000000000..1dd000572 --- /dev/null +++ b/sub-02/ses-010/anat/sub-02_ses-010_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:26:53.030000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0411452, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 286.738 +} \ No newline at end of file diff --git a/sub-02/ses-010/anat/sub-02_ses-010_acq-axial_localizer.nii.gz b/sub-02/ses-010/anat/sub-02_ses-010_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..65cac291f --- /dev/null +++ b/sub-02/ses-010/anat/sub-02_ses-010_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/0f/q8/MD5E-s187450--34a9b0d65731796950c54f00d7aa9ba5.nii.gz/MD5E-s187450--34a9b0d65731796950c54f00d7aa9ba5.nii.gz \ No newline at end of file diff --git a/sub-02/ses-010/anat/sub-02_ses-010_acq-coronal_localizer.json b/sub-02/ses-010/anat/sub-02_ses-010_acq-coronal_localizer.json new file mode 100644 index 000000000..85065900b --- /dev/null +++ b/sub-02/ses-010/anat/sub-02_ses-010_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:27:0.020000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, 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"998ac1dc-5b6f-4180-9d7b-e10a4fda11e4||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz new file mode 120000 index 000000000..c82dcf552 --- /dev/null +++ b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/f9/2Z/MD5E-s1103189--82eefea104e5a499c9122d8337ee68a0.nii.gz/MD5E-s1103189--82eefea104e5a499c9122d8337ee68a0.nii.gz \ No newline at end of file diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.json new file mode 100644 index 000000000..c1395785b --- /dev/null +++ b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.json @@ -0,0 +1,149 @@ +{ + 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+} \ No newline at end of file diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz new file mode 120000 index 000000000..4ba331c22 --- /dev/null +++ b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/9F/p4/MD5E-s1139448--d55ee877003cac24d437a5dd38eecf5b.nii.gz/MD5E-s1139448--d55ee877003cac24d437a5dd38eecf5b.nii.gz \ No newline at end of file diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json new file mode 100644 index 000000000..5a895e3fc --- /dev/null +++ b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json @@ -0,0 +1,152 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:40:24.470000", + 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a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz new file mode 120000 index 000000000..8ee1d97f7 --- /dev/null +++ b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/jG/6P/MD5E-s1103209--72a2a3f14db65547a759b4ce503a2a8e.nii.gz/MD5E-s1103209--72a2a3f14db65547a759b4ce503a2a8e.nii.gz \ No newline at end of file diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.json new file mode 100644 index 000000000..afa588680 --- /dev/null +++ b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.json @@ -0,0 +1,149 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:49:8.572500", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Single-band reference", + "ImageOrientationPatientDICOM": [ + 0.998578, + -0.00516706, + 0.0530537, + 0.0336497, + 0.833015, + -0.552226 + ], + "ImageOrientationText": "Tra>Cor(-33.6)>Sag(2.4)", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "ND", + "MOSAIC" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + 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"SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 286.738, + "dcmmeta_affine": [ + [-1.9971566200256348, 0.06729941815137863, 0.082682304084301, 101.68578338623047], + [0.010334121994674206, 1.6660302877426147, -1.1064521074295044, -46.56220626831055], + [0.10610740631818771, 1.1044517755508423, 1.66400945186615, -92.40599060058594], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 64a34171db9fdad5a4b67c27dd8ec6e8f09b6e5b Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:04:49 -0400 Subject: [PATCH 180/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..c6fd4e89e --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 30d2cbaf-5c39-466c-bc70-787b86658f45 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..3ef0b999f --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 3ef0b999f3e663e508f38083feab07ad4991a453 From 49111533968f753f51402a64830889a78cd096bc Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:05:00 -0400 Subject: [PATCH 181/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-019_acq-axial_localizer.json | 81 +++ .../sub-01_ses-019_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-019_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-019_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-019_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-019_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-019/anat/sub-01_ses-019_scout.json | 542 ++++++++++++++++++ .../ses-019/anat/sub-01_ses-019_scout.nii.gz | 1 + ...9_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-019_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...19_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...019_task-mario3_run-01_part-mag_events.tsv | 1 + ...019_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...19_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-01_part-phase_events.tsv | 1 + ...9_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-019_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...19_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...019_task-mario3_run-02_part-mag_events.tsv | 1 + ...019_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...19_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-02_part-phase_events.tsv | 1 + ...9_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-019_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...19_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...019_task-mario3_run-03_part-mag_events.tsv | 1 + ...019_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...19_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-03_part-phase_events.tsv | 1 + ...9_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-01/ses-019/sub-01_ses-019_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-019/anat/sub-01_ses-019_acq-axial_localizer.json create mode 120000 sub-01/ses-019/anat/sub-01_ses-019_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-019/anat/sub-01_ses-019_acq-coronal_localizer.json create mode 120000 sub-01/ses-019/anat/sub-01_ses-019_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-019/anat/sub-01_ses-019_acq-sagittal_localizer.json create mode 120000 sub-01/ses-019/anat/sub-01_ses-019_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-019/anat/sub-01_ses-019_scout.json create mode 120000 sub-01/ses-019/anat/sub-01_ses-019_scout.nii.gz create mode 100644 sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-01/ses-019/sub-01_ses-019_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 6633341ca..112d31416 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 6633341cac1b0346290e362f2502ac3b5ca8afb2 +Subproject commit 112d3141653307f5d958687f46264a09d7751c8a diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-019/anat/sub-01_ses-019_acq-axial_localizer.json b/sub-01/ses-019/anat/sub-01_ses-019_acq-axial_localizer.json new file mode 100644 index 000000000..94ac251c2 --- /dev/null +++ b/sub-01/ses-019/anat/sub-01_ses-019_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "17:12:54.037500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": 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b/sub-01/ses-019/anat/sub-01_ses-019_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "17:13:1.027500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + 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"SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 275.805 +} \ No newline at end of file diff --git a/sub-01/ses-019/anat/sub-01_ses-019_acq-coronal_localizer.nii.gz b/sub-01/ses-019/anat/sub-01_ses-019_acq-coronal_localizer.nii.gz new file mode 120000 index 000000000..5783574e6 --- /dev/null +++ b/sub-01/ses-019/anat/sub-01_ses-019_acq-coronal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/QV/w2/MD5E-s195750--1ee9ada8cd58b39ae7a29485851d356c.nii.gz/MD5E-s195750--1ee9ada8cd58b39ae7a29485851d356c.nii.gz \ No newline at end of file diff --git a/sub-01/ses-019/anat/sub-01_ses-019_acq-sagittal_localizer.json b/sub-01/ses-019/anat/sub-01_ses-019_acq-sagittal_localizer.json new file mode 100644 index 000000000..8352ece79 --- /dev/null +++ b/sub-01/ses-019/anat/sub-01_ses-019_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "17:12:47.047500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 0, + 1, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Sag", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + 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a/sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-phase_sbref.nii.gz b/sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-phase_sbref.nii.gz new file mode 120000 index 000000000..27b5eeb7d --- /dev/null +++ b/sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/jp/KJ/MD5E-s1103865--fcd5ab480027c3be915cdf6c4f4e142e.nii.gz/MD5E-s1103865--fcd5ab480027c3be915cdf6c4f4e142e.nii.gz \ No newline at end of file diff --git a/sub-01/ses-019/sub-01_ses-019_scans.tsv b/sub-01/ses-019/sub-01_ses-019_scans.tsv new file mode 120000 index 000000000..1d4869684 --- /dev/null +++ b/sub-01/ses-019/sub-01_ses-019_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/7Z/kK/MD5E-s2667--b69660a095db14843e052893384c10da.tsv/MD5E-s2667--b69660a095db14843e052893384c10da.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..2dcf79204 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.994341, 0.105607, 0.0115233, -0.0950436, 0.93281, -0.34761], + "ImageOrientationText": "Tra>Cor(-20.2)>Sag(2.7)", + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0664354, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [610, -7197, -8817, 657, 89, -51, -48, 12], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 275.805, + "dcmmeta_affine": [ + [-1.9886822700500488, -0.190087229013443, 0.09491832554340363, 112.41594696044922], + [-0.2112143337726593, 1.8656196594238281, -0.6890947818756104, -56.83516311645508], + [0.023046694695949554, 0.6952193379402161, 1.8751370906829834, -63.97115707397461], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 247d56baad5732fe8ac8d9ed2fd5191a75edfbd5 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:05:03 -0400 Subject: [PATCH 182/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..8f667489f --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = b4b77db7-f9c1-4be0-8b4b-fd8e89a3aaa1 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..f8716992b --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit f8716992b0790f0ad2e201112a5848de8bbac254 From 0aa945aee5a308890820790568ff2be535192522 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:05:08 -0400 Subject: [PATCH 183/463] fix fmap phase --- ...2_ses-010_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-010_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-010_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-010_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-010_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-010_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-02/ses-010/sub-02_ses-010_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-02/ses-010/fmap/{sub-02_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-010_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-010/fmap/{sub-02_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-010_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-010/fmap/{sub-02_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-010_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-010/fmap/{sub-02_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-010_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-010/fmap/{sub-02_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-010_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-010/fmap/{sub-02_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-010_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-010/fmap/{sub-02_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-010_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-010/fmap/{sub-02_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-010_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-010/fmap/{sub-02_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-010_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-010/fmap/{sub-02_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-010_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index b3eb41139..000000000 --- a/sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:27:56.615000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, 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1.275, 0.5875, 1.3725, 0.685, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 286.738, - "WipMemBlock": "f885fd9c-814c-483a-a037-d2b1d7e95ecf||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9971566200256348, 0.06729941815137863, 0.082682304084301, 101.68578338623047], - [0.010334121994674206, 1.6660302877426147, -1.1064521074295044, -46.56220626831055], - [0.10610740631818771, 1.1044517755508423, 1.66400945186615, -92.40599060058594], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99857829247016, -0.00516706094, 0.05305370193141, 0.03364970804831, 0.83301516244276, -0.5522258924469], - "ImagePositionPatient": [-860.07960431501, -727.71233514142, 384.74990119599], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.258765, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "112606.987000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.0483309357744, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "112843.142000", - "SliceLocation": -46.918986491474, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999813831, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "112606.924000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["112756.615000", "112758.105000", "112759.595000"], - "ContentTime": ["112843.144000", "112843.146000", "112843.149000"], - "InstanceCreationTime": ["112843.144000", "112843.146000", "112843.149000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4746.0, 4742.0, 4746.0], - "WindowWidth": [18536.0, 18534.0, 18540.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 2dfc853bc..000000000 --- a/sub-02/ses-010/fmap/sub-02_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/q4/1K/MD5E-s3333196--31f99bf0f7312f8541d4230fe2b476e0.nii.gz/MD5E-s3333196--31f99bf0f7312f8541d4230fe2b476e0.nii.gz \ No newline at end of file diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 79463563f..000000000 --- a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:27:46.185000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998578, - -0.00516706, - 0.0530537, - 0.0336497, - 0.833015, - -0.552226 - ], - "ImageOrientationText": "Tra>Cor(-33.6)>Sag(2.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0483309, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 627, - -7194, - -8873, - 220, - 36, - -201, - -1, - 44 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 286.738, - "WipMemBlock": "f885fd9c-814c-483a-a037-d2b1d7e95ecf||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 323539b74..000000000 --- a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Zv/gf/MD5E-s1112075--d33f17889196f150323368d5e1843c23.nii.gz/MD5E-s1112075--d33f17889196f150323368d5e1843c23.nii.gz \ No newline at end of file diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index b2fd545d4..000000000 --- a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:28:53.510000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998578, - -0.00516706, - 0.0530537, - 0.0336497, - 0.833015, - -0.552226 - ], - "ImageOrientationText": "Tra>Cor(-33.6)>Sag(2.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0606028, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 627, - -7194, - -8873, - 220, - 36, - -201, - -1, - 44 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 286.738, - "WipMemBlock": "998ac1dc-5b6f-4180-9d7b-e10a4fda11e4||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index c82dcf552..000000000 --- a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/f9/2Z/MD5E-s1103189--82eefea104e5a499c9122d8337ee68a0.nii.gz/MD5E-s1103189--82eefea104e5a499c9122d8337ee68a0.nii.gz \ No newline at end of file diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 5a895e3fc..000000000 --- a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:40:24.470000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998578, - -0.00516706, - 0.0530537, - 0.0336497, - 0.833015, - -0.552226 - ], - "ImageOrientationText": "Tra>Cor(-33.6)>Sag(2.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0606028, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 627, - -7194, - -8873, - 220, - 36, - -201, - -1, - 44 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 286.738, - "WipMemBlock": "a0532b4d-cd8e-4ab4-9fef-86ee9786f7e8||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 8ee1d97f7..000000000 --- a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/jG/6P/MD5E-s1103209--72a2a3f14db65547a759b4ce503a2a8e.nii.gz/MD5E-s1103209--72a2a3f14db65547a759b4ce503a2a8e.nii.gz \ No newline at end of file diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 4e9e1ea81..000000000 --- a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:49:8.572500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998578, - -0.00516706, - 0.0530537, - 0.0336497, - 0.833015, - -0.552226 - ], - "ImageOrientationText": "Tra>Cor(-33.6)>Sag(2.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0606028, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 627, - -7194, - -8873, - 220, - 36, - -201, - -1, - 44 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 286.738, - "WipMemBlock": "8579154f-0319-4290-8f47-0065e05094e4||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index b3348f569..000000000 --- a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/7v/G2/MD5E-s1103318--8ad568636ec18b3c02e29c901d916201.nii.gz/MD5E-s1103318--8ad568636ec18b3c02e29c901d916201.nii.gz \ No newline at end of file diff --git a/sub-02/ses-010/sub-02_ses-010_scans.tsv b/sub-02/ses-010/sub-02_ses-010_scans.tsv index ee18ef068..0b44d48af 120000 --- a/sub-02/ses-010/sub-02_ses-010_scans.tsv +++ b/sub-02/ses-010/sub-02_ses-010_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/3z/93/MD5E-s2667--993c299b4491e6956729d9a34bcc2d42.tsv/MD5E-s2667--993c299b4491e6956729d9a34bcc2d42.tsv \ No newline at end of file +../../.git/annex/objects/ZF/vm/MD5E-s2066--e22891d83191becbdb82851e91404d8a.tsv/MD5E-s2066--e22891d83191becbdb82851e91404d8a.tsv \ No newline at end of file From 679c022955338a50c4a1ad07035585079c190623 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:05:13 -0400 Subject: [PATCH 184/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..ff8fdc6db --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 677f3326-ad36-41e0-8821-52cc3f43481e diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..27698bbc7 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 27698bbc7454feab27b46ff75092f957f104612c From f443994c192655968e33497ee47d8aef400baafb Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:05:14 -0400 Subject: [PATCH 185/463] fix complex event files --- ...g_events.tsv => sub-02_ses-010_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-02_ses-010_task-mario3_run-02_events.tsv} | 0 .../func/sub-02_ses-010_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-02_ses-010_task-mario3_run-03_events.tsv} | 0 .../func/sub-02_ses-010_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-02_ses-010_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-02/ses-010/func/{sub-02_ses-010_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-010_task-mario3_run-01_events.tsv} (100%) rename sub-02/ses-010/func/{sub-02_ses-010_task-mario3_run-01_part-phase_events.tsv => sub-02_ses-010_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_part-phase_events.tsv rename sub-02/ses-010/func/{sub-02_ses-010_task-mario3_run-02_part-mag_events.tsv => sub-02_ses-010_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_events.tsv similarity index 100% rename from sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_part-phase_events.tsv rename to sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_events.tsv diff --git a/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_part-phase_events.tsv b/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_part-mag_events.tsv b/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_events.tsv similarity index 100% rename from sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_part-mag_events.tsv rename to sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_events.tsv diff --git a/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_part-mag_events.tsv b/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 6507e48cab828978191d238cecb986a2ee5d28ec Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:05:27 -0400 Subject: [PATCH 186/463] fix fmap phase --- ...1_ses-019_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-019_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-019_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-019_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-019_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-019_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-019_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-019_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-019_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-019_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-01/ses-019/sub-01_ses-019_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-01/ses-019/fmap/{sub-01_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-019_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-019/fmap/{sub-01_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-019_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-019/fmap/{sub-01_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-019_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-019/fmap/{sub-01_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-019_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-019/fmap/{sub-01_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-019_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-019/fmap/{sub-01_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-019_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-019/fmap/{sub-01_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-019_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-019/fmap/{sub-01_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-019_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-01/ses-019/fmap/{sub-01_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-01_ses-019_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-01/ses-019/fmap/{sub-01_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-01_ses-019_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index e0be33d0f..000000000 --- a/sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "17:14:7.912500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.994341, 0.105607, 0.0115233, -0.0950436, 0.93281, -0.34761], - "ImageOrientationText": 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0.0529824552348, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "171456.287000", - "SliceLocation": -35.059768890139, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000110439, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "171158.867000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["171407.912500", "171409.402500", "171410.892500"], - "ContentTime": ["171456.289000", "171456.297000", "171456.299000"], - "InstanceCreationTime": ["171456.289000", "171456.297000", "171456.299000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4830.0, 4856.0, 4830.0], - "WindowWidth": [18590.0, 18616.0, 18584.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 947fed162..000000000 --- a/sub-01/ses-019/fmap/sub-01_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/xm/Qq/MD5E-s3335320--bbf4743d8735bca45b08dadbfe6a38cc.nii.gz/MD5E-s3335320--bbf4743d8735bca45b08dadbfe6a38cc.nii.gz \ No newline at end of file diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 37753f792..000000000 --- a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "17:13:57.482500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994341, - 0.105607, - 0.0115233, - -0.0950436, - 0.93281, - -0.34761 - ], - "ImageOrientationText": "Tra>Cor(-20.2)>Sag(2.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": 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f55394010..000000000 --- a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/M9/Zz/MD5E-s1112299--316b0766ce5a39661f1993915770b925.nii.gz/MD5E-s1112299--316b0766ce5a39661f1993915770b925.nii.gz \ No newline at end of file diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 46ab8ae1f..000000000 --- a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "17:15:28.887500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - 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- "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0664354, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 610, - -7197, - -8817, - 657, - 89, - -51, - -48, - 12 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 275.805, - "WipMemBlock": "b4495d90-dd50-46f3-aae7-b5cd0b889ae0||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 097cf7faa..000000000 --- a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/JQ/F0/MD5E-s1103864--d8363f349bc60356388118475edc4267.nii.gz/MD5E-s1103864--d8363f349bc60356388118475edc4267.nii.gz \ No newline at end of file diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 0b0e5a336..000000000 --- a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "17:27:37.897500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994341, - 0.105607, - 0.0115233, - -0.0950436, - 0.93281, - -0.34761 - ], - "ImageOrientationText": "Tra>Cor(-20.2)>Sag(2.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0664354, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 610, - -7197, - -8817, - 657, - 89, - -51, - -48, - 12 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 275.805, - "WipMemBlock": "9c0817d9-c03a-4207-b95f-1c60ae9032b1||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 7781c195a..000000000 --- a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/kj/w7/MD5E-s1103691--8522a76e4d3ceb605293c364d9fc7086.nii.gz/MD5E-s1103691--8522a76e4d3ceb605293c364d9fc7086.nii.gz \ No newline at end of file diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index c3f8c1f23..000000000 --- a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "17:38:21.500000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994341, - 0.105607, - 0.0115233, - -0.0950436, - 0.93281, - -0.34761 - ], - "ImageOrientationText": "Tra>Cor(-20.2)>Sag(2.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0664354, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 610, - -7197, - -8817, - 657, - 89, - -51, - -48, - 12 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 275.805, - "WipMemBlock": "a2b3aea1-681e-4780-8379-269e93a1eb71||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 27b5eeb7d..000000000 --- a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/jp/KJ/MD5E-s1103865--fcd5ab480027c3be915cdf6c4f4e142e.nii.gz/MD5E-s1103865--fcd5ab480027c3be915cdf6c4f4e142e.nii.gz \ No newline at end of file diff --git a/sub-01/ses-019/sub-01_ses-019_scans.tsv b/sub-01/ses-019/sub-01_ses-019_scans.tsv index 1d4869684..e00b40e2a 120000 --- a/sub-01/ses-019/sub-01_ses-019_scans.tsv +++ b/sub-01/ses-019/sub-01_ses-019_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/7Z/kK/MD5E-s2667--b69660a095db14843e052893384c10da.tsv/MD5E-s2667--b69660a095db14843e052893384c10da.tsv \ No newline at end of file +../../.git/annex/objects/j6/Fz/MD5E-s2066--54ed51f45f0c0e80205dcd00257c9429.tsv/MD5E-s2066--54ed51f45f0c0e80205dcd00257c9429.tsv \ No newline at end of file From af311c9b5e13a277d7eda2421af73a0ece45492a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:05:34 -0400 Subject: [PATCH 187/463] fix complex event files --- ...g_events.tsv => sub-01_ses-019_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-019_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-019_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-01_ses-019_task-mario3_run-03_events.tsv} | 0 .../func/sub-01_ses-019_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-01_ses-019_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-01/ses-019/func/{sub-01_ses-019_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-019_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-019/func/{sub-01_ses-019_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-019_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-02_part-phase_events.tsv rename sub-01/ses-019/func/{sub-01_ses-019_task-mario3_run-02_part-mag_events.tsv => sub-01_ses-019_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_events.tsv similarity index 100% rename from sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-02_part-mag_events.tsv rename to sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_events.tsv diff --git a/sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-mag_events.tsv b/sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-019/func/sub-01_ses-019_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 9a4bdf4d8317809d595ef6070109019e99438684 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:05:36 -0400 Subject: [PATCH 188/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-03_ses-012_acq-axial_localizer.json | 81 +++ .../sub-03_ses-012_acq-axial_localizer.nii.gz | 1 + .../sub-03_ses-012_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-012_acq-coronal_localizer.nii.gz | 1 + ...sub-03_ses-012_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-012_acq-sagittal_localizer.nii.gz | 1 + sub-03/ses-012/anat/sub-03_ses-012_scout.json | 542 ++++++++++++++++++ .../ses-012/anat/sub-03_ses-012_scout.nii.gz | 1 + ...2_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ...-012_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...12_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...012_task-mario3_run-01_part-mag_events.tsv | 1 + ...012_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...12_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-01_part-phase_events.tsv | 1 + ...2_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-012_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...12_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...012_task-mario3_run-02_part-mag_events.tsv | 1 + ...012_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...12_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-02_part-phase_events.tsv | 1 + ...2_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + sub-03/ses-012/sub-03_ses-012_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 51 files changed, 3485 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-012/anat/sub-03_ses-012_acq-axial_localizer.json create mode 120000 sub-03/ses-012/anat/sub-03_ses-012_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-012/anat/sub-03_ses-012_acq-coronal_localizer.json create mode 120000 sub-03/ses-012/anat/sub-03_ses-012_acq-coronal_localizer.nii.gz create mode 100644 sub-03/ses-012/anat/sub-03_ses-012_acq-sagittal_localizer.json create mode 120000 sub-03/ses-012/anat/sub-03_ses-012_acq-sagittal_localizer.nii.gz create mode 100644 sub-03/ses-012/anat/sub-03_ses-012_scout.json create mode 120000 sub-03/ses-012/anat/sub-03_ses-012_scout.nii.gz create mode 100644 sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_part-phase_sbref.nii.gz create mode 120000 sub-03/ses-012/sub-03_ses-012_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 27698bbc7..af785dc0d 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 27698bbc7454feab27b46ff75092f957f104612c +Subproject commit af785dc0d5103b5d2d4a7556853b14b51e33cb04 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-03/ses-012/anat/sub-03_ses-012_acq-axial_localizer.json b/sub-03/ses-012/anat/sub-03_ses-012_acq-axial_localizer.json new file mode 100644 index 000000000..47598ea88 --- /dev/null +++ b/sub-03/ses-012/anat/sub-03_ses-012_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "14:02:25.005000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0437884, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 248.771 +} \ No newline at end of file diff --git a/sub-03/ses-012/anat/sub-03_ses-012_acq-axial_localizer.nii.gz b/sub-03/ses-012/anat/sub-03_ses-012_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..e977f900a --- /dev/null +++ b/sub-03/ses-012/anat/sub-03_ses-012_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/X4/FP/MD5E-s163671--3e06b7983ed110bfac5d09432040125c.nii.gz/MD5E-s163671--3e06b7983ed110bfac5d09432040125c.nii.gz \ No newline at end of file diff --git a/sub-03/ses-012/anat/sub-03_ses-012_acq-coronal_localizer.json b/sub-03/ses-012/anat/sub-03_ses-012_acq-coronal_localizer.json new file mode 100644 index 000000000..daceb1bf1 --- /dev/null +++ b/sub-03/ses-012/anat/sub-03_ses-012_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "14:02:31.995000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0437884, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 248.771 +} \ No newline at end of file diff --git a/sub-03/ses-012/anat/sub-03_ses-012_acq-coronal_localizer.nii.gz b/sub-03/ses-012/anat/sub-03_ses-012_acq-coronal_localizer.nii.gz new file mode 120000 index 000000000..b52c877e6 --- /dev/null +++ b/sub-03/ses-012/anat/sub-03_ses-012_acq-coronal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/gk/w7/MD5E-s179829--869adaecbece62c4634366430de26d31.nii.gz/MD5E-s179829--869adaecbece62c4634366430de26d31.nii.gz \ No newline at end of file diff --git a/sub-03/ses-012/anat/sub-03_ses-012_acq-sagittal_localizer.json b/sub-03/ses-012/anat/sub-03_ses-012_acq-sagittal_localizer.json new file mode 100644 index 000000000..9e02f7c95 --- /dev/null +++ b/sub-03/ses-012/anat/sub-03_ses-012_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "14:02:18.015000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 0, + 1, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Sag", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0437884, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SliceTiming": [ + 0, + 10.4844, + 3.5 + ], + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 28, + "StationName": "MRC35049", + "TxRefAmp": 248.771 +} \ No newline at end of file diff --git a/sub-03/ses-012/anat/sub-03_ses-012_acq-sagittal_localizer.nii.gz b/sub-03/ses-012/anat/sub-03_ses-012_acq-sagittal_localizer.nii.gz new file mode 120000 index 000000000..919165998 --- /dev/null +++ b/sub-03/ses-012/anat/sub-03_ses-012_acq-sagittal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/2j/zK/MD5E-s578512--f927ad160f3b15e2d7e1a61c781e8985.nii.gz/MD5E-s578512--f927ad160f3b15e2d7e1a61c781e8985.nii.gz \ No newline at end of file diff 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+1,152 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "14:03:15.890000", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTime1": 0.037, + "EchoTime2": 0.001, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Single-band reference", + "ImageOrientationPatientDICOM": [ + 0.999417, + 0.00539741, + 0.0337053, + 0.00261647, + 0.972402, + -0.233299 + ], + "ImageOrientationText": "Tra>Cor(-13.5)>Sag(2.0)", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "P", + "ND", + "MOSAIC", + "PHASE" + ], + 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"1ffb860f-31ba-4803-8d3e-98abe1ec15fb||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz new file mode 120000 index 000000000..df72aa16a --- /dev/null +++ b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Xp/jP/MD5E-s1112235--516ee22e767d0b8e40c4d7ceef9bcb50.nii.gz/MD5E-s1112235--516ee22e767d0b8e40c4d7ceef9bcb50.nii.gz \ No newline at end of file diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json new file mode 100644 index 000000000..3ddf42d79 --- /dev/null +++ b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json @@ -0,0 +1,149 @@ +{ + 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+} \ No newline at end of file diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz new file mode 120000 index 000000000..b30c1414f --- /dev/null +++ b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/fp/X6/MD5E-s1093785--b188c853003fad90ea0ef90b8709e7ed.nii.gz/MD5E-s1093785--b188c853003fad90ea0ef90b8709e7ed.nii.gz \ No newline at end of file diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json new file mode 100644 index 000000000..3716c9775 --- /dev/null +++ b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json @@ -0,0 +1,152 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "14:04:15.310000", + 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a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz new file mode 120000 index 000000000..10f849117 --- /dev/null +++ b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Jf/q3/MD5E-s1103596--3f0359f6e0aae9b1844da0b4abe57f73.nii.gz/MD5E-s1103596--3f0359f6e0aae9b1844da0b4abe57f73.nii.gz \ No newline at end of file diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json new file mode 100644 index 000000000..36df49ed9 --- /dev/null +++ b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json @@ -0,0 +1,149 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "14:18:16.115000", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + 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newline at end of file From 774cce91f10ec2de8d7b07dc830dd92f68345ae0 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:05:37 -0400 Subject: [PATCH 189/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-03_ses-008_acq-axial_localizer.json | 81 +++ .../sub-03_ses-008_acq-axial_localizer.nii.gz | 1 + .../sub-03_ses-008_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-008_acq-coronal_localizer.nii.gz | 1 + ...sub-03_ses-008_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-008_acq-sagittal_localizer.nii.gz | 1 + sub-03/ses-008/anat/sub-03_ses-008_scout.json | 542 ++++++++++++++++++ .../ses-008/anat/sub-03_ses-008_scout.nii.gz | 1 + ...8_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-008_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-01_part-mag_events.tsv | 1 + ...008_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-01_part-phase_events.tsv | 1 + ...8_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-008_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-02_part-mag_events.tsv | 1 + ...008_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-02_part-phase_events.tsv | 1 + ...8_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-008_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-03_part-mag_events.tsv | 1 + ...008_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-03_part-phase_events.tsv | 1 + ...8_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-008_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-04_part-mag_events.tsv | 1 + ...008_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-04_part-phase_events.tsv | 1 + ...8_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-03/ses-008/sub-03_ses-008_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5409 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-008/anat/sub-03_ses-008_acq-axial_localizer.json create mode 120000 sub-03/ses-008/anat/sub-03_ses-008_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-008/anat/sub-03_ses-008_acq-coronal_localizer.json create mode 120000 sub-03/ses-008/anat/sub-03_ses-008_acq-coronal_localizer.nii.gz create mode 100644 sub-03/ses-008/anat/sub-03_ses-008_acq-sagittal_localizer.json create mode 120000 sub-03/ses-008/anat/sub-03_ses-008_acq-sagittal_localizer.nii.gz create mode 100644 sub-03/ses-008/anat/sub-03_ses-008_scout.json create mode 120000 sub-03/ses-008/anat/sub-03_ses-008_scout.nii.gz create mode 100644 sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_part-phase_sbref.nii.gz create mode 120000 sub-03/ses-008/sub-03_ses-008_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index f8716992b..8f58be26f 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit f8716992b0790f0ad2e201112a5848de8bbac254 +Subproject commit 8f58be26fc4569ae02ab91f3e76be5d1a57b715e diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-03/ses-008/anat/sub-03_ses-008_acq-axial_localizer.json b/sub-03/ses-008/anat/sub-03_ses-008_acq-axial_localizer.json new file mode 100644 index 000000000..ffeb6b7be --- /dev/null +++ b/sub-03/ses-008/anat/sub-03_ses-008_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "13:51:10.987500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0483015, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 262.346 +} \ No newline at end of file diff --git a/sub-03/ses-008/anat/sub-03_ses-008_acq-axial_localizer.nii.gz b/sub-03/ses-008/anat/sub-03_ses-008_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..3905fdc3d --- /dev/null +++ b/sub-03/ses-008/anat/sub-03_ses-008_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/kw/F7/MD5E-s166234--c803a640e4eb891fef0f191cca1eed04.nii.gz/MD5E-s166234--c803a640e4eb891fef0f191cca1eed04.nii.gz \ No newline at end of file diff --git a/sub-03/ses-008/anat/sub-03_ses-008_acq-coronal_localizer.json b/sub-03/ses-008/anat/sub-03_ses-008_acq-coronal_localizer.json new file mode 100644 index 000000000..9ef63407c --- /dev/null +++ b/sub-03/ses-008/anat/sub-03_ses-008_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "13:51:17.977500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + 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"AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.99992, 0.0059029, 0.0111662, -0.00296681, 0.969104, -0.246634], + "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.7)", + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0711433, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [616, -7224, -8757, 695, 52, -3, 29, -25], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 262.346, + "dcmmeta_affine": [ + [-1.999840497970581, -0.005933612119406462, 0.024554096162319183, 108.77191925048828], + [-0.011805800721049309, 1.9382084608078003, -0.493161678314209, -74.79946899414062], + [0.022332364693284035, 0.4932672679424286, 1.9380888938903809, -53.7884521484375], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 21334d840b8631c93fa18e45c5170473f9ff8b0b Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:05:59 -0400 Subject: [PATCH 190/463] fill IntendedFor --- ...2_ses-010_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...2_ses-010_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...2_ses-010_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...2_ses-010_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_epi.json index 6a0a1a78b..947a23efe 100644 --- a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998578, - -0.00516706, - 0.0530537, - 0.0336497, - 0.833015, - -0.552226 - ], + "ImageOrientationPatientDICOM": [0.998578, -0.00516706, 0.0530537, 0.0336497, 0.833015, -0.552226], "ImageOrientationText": "Tra>Cor(-33.6)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-02_ses-010_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-010/func/sub-02_ses-010_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-010/func/sub-02_ses-010_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 627, - -7194, - -8873, - 220, - 36, - -201, - -1, - 44 - ], + "ShimSetting": [627, -7194, -8873, 220, 36, -201, -1, 44], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_epi.json b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_epi.json index 49c821005..3c5f3147c 100644 --- a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998578, - -0.00516706, - 0.0530537, - 0.0336497, - 0.833015, - -0.552226 - ], + "ImageOrientationPatientDICOM": [0.998578, -0.00516706, 0.0530537, 0.0336497, 0.833015, -0.552226], "ImageOrientationText": "Tra>Cor(-33.6)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-02_ses-010_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 627, - -7194, - -8873, - 220, - 36, - -201, - -1, - 44 - ], + "ShimSetting": [627, -7194, -8873, 220, 36, -201, -1, 44], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_epi.json b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_epi.json index c1395785b..b1fdb1cae 100644 --- a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998578, - -0.00516706, - 0.0530537, - 0.0336497, - 0.833015, - -0.552226 - ], + "ImageOrientationPatientDICOM": [0.998578, -0.00516706, 0.0530537, 0.0336497, 0.833015, -0.552226], "ImageOrientationText": "Tra>Cor(-33.6)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-02_ses-010_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 627, - -7194, - -8873, - 220, - 36, - -201, - -1, - 44 - ], + "ShimSetting": [627, -7194, -8873, 220, 36, -201, -1, 44], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.02, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_epi.json b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_epi.json index afa588680..9783bd097 100644 --- a/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-02/ses-010/fmap/sub-02_ses-010_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998578, - -0.00516706, - 0.0530537, - 0.0336497, - 0.833015, - -0.552226 - ], + "ImageOrientationPatientDICOM": [0.998578, -0.00516706, 0.0530537, 0.0336497, 0.833015, -0.552226], "ImageOrientationText": "Tra>Cor(-33.6)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-02_ses-010_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 627, - -7194, - -8873, - 220, - 36, - -201, - -1, - 44 - ], + "ShimSetting": [627, -7194, -8873, 220, 36, -201, -1, 44], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 32b463c97d83687eebf77661ccd710b47868f08b Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:06:03 -0400 Subject: [PATCH 191/463] fix fmap phase --- ...3_ses-012_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-012_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-012_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-012_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-012_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-012_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-012_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-012_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - sub-03/ses-012/sub-03_ses-012_scans.tsv | 2 +- 17 files changed, 1 insertion(+), 638 deletions(-) rename sub-03/ses-012/fmap/{sub-03_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-012_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-012/fmap/{sub-03_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-012_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-012/fmap/{sub-03_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-012_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-012/fmap/{sub-03_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-012_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-012/fmap/{sub-03_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-012_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-012/fmap/{sub-03_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-012_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-012/fmap/{sub-03_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-012_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-012/fmap/{sub-03_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-012_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 0b04b23e0..000000000 --- a/sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:03:26.320000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999417, 0.00539741, 0.0337053, 0.00261647, 0.972402, -0.233299], - "ImageOrientationText": "Tra>Cor(-13.5)>Sag(2.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - 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a/sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 23241ea52..000000000 --- a/sub-03/ses-012/fmap/sub-03_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/v2/V0/MD5E-s3334491--fbe99bba5c7cad271a9543b9ef63f791.nii.gz/MD5E-s3334491--fbe99bba5c7cad271a9543b9ef63f791.nii.gz \ No newline at end of file diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index f3cc368c9..000000000 --- a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:03:15.890000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999417, - 0.00539741, - 0.0337053, - 0.00261647, - 0.972402, - -0.233299 - ], - "ImageOrientationText": "Tra>Cor(-13.5)>Sag(2.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - 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a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Xp/jP/MD5E-s1112235--516ee22e767d0b8e40c4d7ceef9bcb50.nii.gz/MD5E-s1112235--516ee22e767d0b8e40c4d7ceef9bcb50.nii.gz \ No newline at end of file diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 3716c9775..000000000 --- a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:04:15.310000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": 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"ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0644959, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 630, - -7229, - -8796, - 709, - 79, - -10, - 54, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 248.771, - "WipMemBlock": "5c3a0c63-dabb-44bd-8b8a-c91d714c3f43||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 10f849117..000000000 --- a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Jf/q3/MD5E-s1103596--3f0359f6e0aae9b1844da0b4abe57f73.nii.gz/MD5E-s1103596--3f0359f6e0aae9b1844da0b4abe57f73.nii.gz \ No newline at end of file diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 15fc670a3..000000000 --- a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:18:16.115000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999417, - 0.00539741, - 0.0337053, - 0.00261647, - 0.972402, - -0.233299 - ], - "ImageOrientationText": "Tra>Cor(-13.5)>Sag(2.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0644959, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 630, - -7229, - -8796, - 709, - 79, - -10, - 54, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 248.771, - "WipMemBlock": "b773826a-4f42-4c0a-bfb9-ba549014f5a9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 5092e0216..000000000 --- a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/9j/fG/MD5E-s1103591--b9bc6fc94f1af39cd793e687a5736546.nii.gz/MD5E-s1103591--b9bc6fc94f1af39cd793e687a5736546.nii.gz \ No newline at end of file diff --git a/sub-03/ses-012/sub-03_ses-012_scans.tsv b/sub-03/ses-012/sub-03_ses-012_scans.tsv index 48c32b930..df17479c8 120000 --- a/sub-03/ses-012/sub-03_ses-012_scans.tsv +++ b/sub-03/ses-012/sub-03_ses-012_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/Mk/mq/MD5E-s2045--00475d2bdec1817e39b8088480bf9f77.tsv/MD5E-s2045--00475d2bdec1817e39b8088480bf9f77.tsv \ No newline at end of file +../../.git/annex/objects/M9/q4/MD5E-s1565--bf7b1c6ac291f68000da0416c6989d49.tsv/MD5E-s1565--bf7b1c6ac291f68000da0416c6989d49.tsv \ No newline at end of file From ddf83d1c5bf7105d2fc3b7e8ca586e4493227f26 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:06:08 -0400 Subject: [PATCH 192/463] fix fmap phase --- ...3_ses-008_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-008_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-008_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-03/ses-008/sub-03_ses-008_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-03/ses-008/fmap/{sub-03_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-008_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-008/fmap/{sub-03_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-008_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-008/fmap/{sub-03_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-008_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-008/fmap/{sub-03_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-008_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-008/fmap/{sub-03_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-008_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-008/fmap/{sub-03_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-008_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-008/fmap/{sub-03_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-008_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-008/fmap/{sub-03_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-008_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-03/ses-008/fmap/{sub-03_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-03_ses-008_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-03/ses-008/fmap/{sub-03_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-03_ses-008_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-03/ses-008/fmap/{sub-03_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-03_ses-008_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-03/ses-008/fmap/{sub-03_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-03_ses-008_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 30bc50695..000000000 --- a/sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:52:15.035000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.99992, 0.0059029, 0.0111662, -0.00296681, 0.969104, -0.246634], - "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.056737, - "ScanOptions": "FS", - "ScanningSequence": 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a/sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index c4419eb30..000000000 --- a/sub-03/ses-008/fmap/sub-03_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/69/z7/MD5E-s3334648--b52fa3519495b4d8a85e801d4b866f2d.nii.gz/MD5E-s3334648--b52fa3519495b4d8a85e801d4b866f2d.nii.gz \ No newline at end of file diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 367898f82..000000000 --- a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:52:4.605000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - 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+++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/4J/V5/MD5E-s1112387--90cec2cdad2c106f39610eb6d298cdf6.nii.gz/MD5E-s1112387--90cec2cdad2c106f39610eb6d298cdf6.nii.gz \ No newline at end of file diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index cbfe8f144..000000000 --- a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:53:10.240000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 39ab5908f..000000000 --- a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - 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"InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0711433, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 616, - -7224, - -8757, - 695, - 52, - -3, - 29, - -25 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 262.346, - "WipMemBlock": "daf9e600-2435-44fc-9867-004d8739bcc9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 411099305..000000000 --- a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Fq/Jf/MD5E-s1103709--76c1fa17b70e8924ba0b1f6c1bcaa2eb.nii.gz/MD5E-s1103709--76c1fa17b70e8924ba0b1f6c1bcaa2eb.nii.gz \ No newline at end of file diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index ba28ee2b0..000000000 --- a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:09:25.637500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99992, - 0.0059029, - 0.0111662, - -0.00296681, - 0.969104, - -0.246634 - ], - "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0711433, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 616, - -7224, - -8757, - 695, - 52, - -3, - 29, - -25 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 262.346, - "WipMemBlock": "60d2223b-b749-4da4-a1ce-1c55c8d2f994||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 2bcc55065..000000000 --- a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Q8/Z5/MD5E-s1103734--40d3c34368b0b5a241ead9c1f1b67468.nii.gz/MD5E-s1103734--40d3c34368b0b5a241ead9c1f1b67468.nii.gz \ No newline at end of file diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 94e53b219..000000000 --- a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:18:51.485000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99992, - 0.0059029, - 0.0111662, - -0.00296681, - 0.969104, - -0.246634 - ], - "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0711433, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 616, - -7224, - -8757, - 695, - 52, - -3, - 29, - -25 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 262.346, - "WipMemBlock": "08ccd776-715a-4325-89ac-428182ae3724||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index af48eb328..000000000 --- a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/4v/9F/MD5E-s1103933--961743fe0f416d8b56df610338cb3ded.nii.gz/MD5E-s1103933--961743fe0f416d8b56df610338cb3ded.nii.gz \ No newline at end of file diff --git a/sub-03/ses-008/sub-03_ses-008_scans.tsv b/sub-03/ses-008/sub-03_ses-008_scans.tsv index b56b1afaf..544d8c803 120000 --- a/sub-03/ses-008/sub-03_ses-008_scans.tsv +++ b/sub-03/ses-008/sub-03_ses-008_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/Pv/Wj/MD5E-s3289--82e8852b92e77c13f114dc29be682396.tsv/MD5E-s3289--82e8852b92e77c13f114dc29be682396.tsv \ No newline at end of file +../../.git/annex/objects/Q4/8v/MD5E-s2567--6ba7e82fcd59b4a6f7c2a4bf1d4e5afe.tsv/MD5E-s2567--6ba7e82fcd59b4a6f7c2a4bf1d4e5afe.tsv \ No newline at end of file From 1aaa3a6329cbbee8b49717e56ff65549b9f394a3 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:06:09 -0400 Subject: [PATCH 193/463] fix complex event files --- ...g_events.tsv => sub-03_ses-012_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-03_ses-012_task-mario3_run-02_events.tsv} | 0 .../func/sub-03_ses-012_task-mario3_run-02_part-mag_events.tsv | 1 - .../func/sub-03_ses-012_task-mario3_run-02_part-phase_events.tsv | 1 - 4 files changed, 2 deletions(-) rename sub-03/ses-012/func/{sub-03_ses-012_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-012_task-mario3_run-01_events.tsv} (100%) rename sub-03/ses-012/func/{sub-03_ses-012_task-mario3_run-01_part-phase_events.tsv => sub-03_ses-012_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_part-mag_events.tsv delete mode 120000 sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_part-phase_events.tsv diff --git a/sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_events.tsv similarity index 100% rename from sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-01_part-phase_events.tsv rename to sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_events.tsv diff --git a/sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_part-mag_events.tsv b/sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_part-phase_events.tsv b/sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-012/func/sub-03_ses-012_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From da880c62cdf007fa71504500d1c1ba89f7b29141 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:06:15 -0400 Subject: [PATCH 194/463] fix complex event files --- ...g_events.tsv => sub-03_ses-008_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-03_ses-008_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-03_ses-008_task-mario3_run-03_events.tsv} | 0 .../func/sub-03_ses-008_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-03_ses-008_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-03_ses-008_task-mario3_run-04_events.tsv} | 0 .../func/sub-03_ses-008_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-03_ses-008_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-03/ses-008/func/{sub-03_ses-008_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-008_task-mario3_run-01_events.tsv} (100%) rename sub-03/ses-008/func/{sub-03_ses-008_task-mario3_run-01_part-phase_events.tsv => sub-03_ses-008_task-mario3_run-02_events.tsv} (100%) rename sub-03/ses-008/func/{sub-03_ses-008_task-mario3_run-02_part-mag_events.tsv => sub-03_ses-008_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_part-phase_events.tsv rename sub-03/ses-008/func/{sub-03_ses-008_task-mario3_run-02_part-phase_events.tsv => sub-03_ses-008_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-02_events.tsv similarity index 100% rename from sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-01_part-phase_events.tsv rename to sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-02_events.tsv diff --git a/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-02_part-mag_events.tsv b/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_events.tsv similarity index 100% rename from sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-02_part-mag_events.tsv rename to sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_events.tsv diff --git a/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_part-mag_events.tsv b/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_part-phase_events.tsv b/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-02_part-phase_events.tsv b/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_events.tsv similarity index 100% rename from sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-02_part-phase_events.tsv rename to sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_events.tsv diff --git a/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_part-mag_events.tsv b/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_part-phase_events.tsv b/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-008/func/sub-03_ses-008_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From c1ffa6ca2338b6bfa2847cc536480aec0f15dc21 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:06:17 -0400 Subject: [PATCH 195/463] fill IntendedFor --- ...1_ses-019_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...1_ses-019_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-019_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...1_ses-019_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_epi.json index 76e6091ee..8241df22b 100644 --- a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994341, - 0.105607, - 0.0115233, - -0.0950436, - 0.93281, - -0.34761 - ], + "ImageOrientationPatientDICOM": [0.994341, 0.105607, 0.0115233, -0.0950436, 0.93281, -0.34761], "ImageOrientationText": "Tra>Cor(-20.2)>Sag(2.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-019/func/sub-01_ses-019_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-019/func/sub-01_ses-019_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-019/func/sub-01_ses-019_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 610, - -7197, - -8817, - 657, - 89, - -51, - -48, - 12 - ], + "ShimSetting": [610, -7197, -8817, 657, 89, -51, -48, 12], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_epi.json index eaadd76da..6030417ea 100644 --- a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994341, - 0.105607, - 0.0115233, - -0.0950436, - 0.93281, - -0.34761 - ], + "ImageOrientationPatientDICOM": [0.994341, 0.105607, 0.0115233, -0.0950436, 0.93281, -0.34761], "ImageOrientationText": "Tra>Cor(-20.2)>Sag(2.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-019/func/sub-01_ses-019_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 610, - -7197, - -8817, - 657, - 89, - -51, - -48, - 12 - ], + "ShimSetting": [610, -7197, -8817, 657, 89, -51, -48, 12], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_epi.json index 8682e0e62..3d5ffb988 100644 --- a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994341, - 0.105607, - 0.0115233, - -0.0950436, - 0.93281, - -0.34761 - ], + "ImageOrientationPatientDICOM": [0.994341, 0.105607, 0.0115233, -0.0950436, 0.93281, -0.34761], "ImageOrientationText": "Tra>Cor(-20.2)>Sag(2.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-019/func/sub-01_ses-019_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 610, - -7197, - -8817, - 657, - 89, - -51, - -48, - 12 - ], + "ShimSetting": [610, -7197, -8817, 657, 89, -51, -48, 12], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_epi.json b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_epi.json index 75cc00bd9..0b9c7b5dc 100644 --- a/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-01/ses-019/fmap/sub-01_ses-019_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994341, - 0.105607, - 0.0115233, - -0.0950436, - 0.93281, - -0.34761 - ], + "ImageOrientationPatientDICOM": [0.994341, 0.105607, 0.0115233, -0.0950436, 0.93281, -0.34761], "ImageOrientationText": "Tra>Cor(-20.2)>Sag(2.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-019/func/sub-01_ses-019_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 610, - -7197, - -8817, - 657, - 89, - -51, - -48, - 12 - ], + "ShimSetting": [610, -7197, -8817, 657, 89, -51, -48, 12], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 550d88ffeeb007347eb7e724363398484862c06e Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:06:40 -0400 Subject: [PATCH 196/463] fill IntendedFor --- ...3_ses-012_acq-sbref_dir-AP_run-01_epi.json | 89 ++----------------- ...3_ses-012_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...3_ses-012_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- 3 files changed, 22 insertions(+), 243 deletions(-) diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_epi.json index dc30879cc..6e72efb40 100644 --- a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999417, - 0.00539741, - 0.0337053, - 0.00261647, - 0.972402, - -0.233299 - ], + "ImageOrientationPatientDICOM": [0.999417, 0.00539741, 0.0337053, 0.00261647, 0.972402, -0.233299], "ImageOrientationText": "Tra>Cor(-13.5)>Sag(2.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,16 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-012/func/sub-03_ses-012_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-012/func/sub-03_ses-012_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +64,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 630, - -7229, - -8796, - 709, - 79, - -10, - 54, - 0 - ], + "ShimSetting": [630, -7229, -8796, 709, 79, -10, 54, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_epi.json b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_epi.json index 3ddf42d79..0b8e4e14d 100644 --- a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999417, - 0.00539741, - 0.0337053, - 0.00261647, - 0.972402, - -0.233299 - ], + "ImageOrientationPatientDICOM": [0.999417, 0.00539741, 0.0337053, 0.00261647, 0.972402, -0.233299], "ImageOrientationText": "Tra>Cor(-13.5)>Sag(2.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-012/func/sub-03_ses-012_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 630, - -7229, - -8796, - 709, - 79, - -10, - 54, - 0 - ], + "ShimSetting": [630, -7229, -8796, 709, 79, -10, 54, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_epi.json b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_epi.json index 36df49ed9..c16fe904f 100644 --- a/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-03/ses-012/fmap/sub-03_ses-012_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999417, - 0.00539741, - 0.0337053, - 0.00261647, - 0.972402, - -0.233299 - ], + "ImageOrientationPatientDICOM": [0.999417, 0.00539741, 0.0337053, 0.00261647, 0.972402, -0.233299], "ImageOrientationText": "Tra>Cor(-13.5)>Sag(2.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-012/func/sub-03_ses-012_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 630, - -7229, - -8796, - 709, - 79, - -10, - 54, - 0 - ], + "ShimSetting": [630, -7229, -8796, 709, 79, -10, 54, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 535eb8edbc9169246c4205eeeb07ee1b8ac5ca8c Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:06:48 -0400 Subject: [PATCH 197/463] fill IntendedFor --- ...3_ses-008_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...3_ses-008_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...3_ses-008_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...3_ses-008_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...3_ses-008_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_epi.json index a5cb51da6..6a5cef2ae 100644 --- a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99992, - 0.0059029, - 0.0111662, - -0.00296681, - 0.969104, - -0.246634 - ], + "ImageOrientationPatientDICOM": [0.99992, 0.0059029, 0.0111662, -0.00296681, 0.969104, -0.246634], "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-03_ses-008_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-008/func/sub-03_ses-008_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-008/func/sub-03_ses-008_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-008/func/sub-03_ses-008_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 616, - -7224, - -8757, - 695, - 52, - -3, - 29, - -25 - ], + "ShimSetting": [616, -7224, -8757, 695, 52, -3, 29, -25], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_epi.json b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_epi.json index 87724bb52..28ae5e710 100644 --- a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99992, - 0.0059029, - 0.0111662, - -0.00296681, - 0.969104, - -0.246634 - ], + "ImageOrientationPatientDICOM": [0.99992, 0.0059029, 0.0111662, -0.00296681, 0.969104, -0.246634], "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-03_ses-008_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 616, - -7224, - -8757, - 695, - 52, - -3, - 29, - -25 - ], + "ShimSetting": [616, -7224, -8757, 695, 52, -3, 29, -25], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_epi.json b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_epi.json index 2e20316c7..c1b7afb98 100644 --- a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99992, - 0.0059029, - 0.0111662, - -0.00296681, - 0.969104, - -0.246634 - ], + "ImageOrientationPatientDICOM": [0.99992, 0.0059029, 0.0111662, -0.00296681, 0.969104, -0.246634], "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-03_ses-008_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 616, - -7224, - -8757, - 695, - 52, - -3, - 29, - -25 - ], + "ShimSetting": [616, -7224, -8757, 695, 52, -3, 29, -25], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_epi.json b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_epi.json index 517abb572..2a3b66f3b 100644 --- a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99992, - 0.0059029, - 0.0111662, - -0.00296681, - 0.969104, - -0.246634 - ], + "ImageOrientationPatientDICOM": [0.99992, 0.0059029, 0.0111662, -0.00296681, 0.969104, -0.246634], "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-03_ses-008_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 616, - -7224, - -8757, - 695, - 52, - -3, - 29, - -25 - ], + "ShimSetting": [616, -7224, -8757, 695, 52, -3, 29, -25], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_epi.json b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_epi.json index d8ab5b8cd..583e9cbf4 100644 --- a/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-03/ses-008/fmap/sub-03_ses-008_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99992, - 0.0059029, - 0.0111662, - -0.00296681, - 0.969104, - -0.246634 - ], + "ImageOrientationPatientDICOM": [0.99992, 0.0059029, 0.0111662, -0.00296681, 0.969104, -0.246634], "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-03_ses-008_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 616, - -7224, - -8757, - 695, - 52, - -3, - 29, - -25 - ], + "ShimSetting": [616, -7224, -8757, 695, 52, -3, 29, -25], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From e08c3a8ecd2a03e4ae2da1d1d624af4cfb9137cb Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:08:58 -0400 Subject: [PATCH 198/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..6a3937dff --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = ac2eea98-b5ec-4ff2-8d20-05aa1b28b703 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..97234517f --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 97234517fdca705c530d63cf0e4226503867458a From 705cd9971abc4678d314b23f285133f171f29532 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:09:24 -0400 Subject: [PATCH 199/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-03_ses-007_acq-axial_localizer.json | 81 +++ .../sub-03_ses-007_acq-axial_localizer.nii.gz | 1 + .../sub-03_ses-007_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-007_acq-coronal_localizer.nii.gz | 1 + ...sub-03_ses-007_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-007_acq-sagittal_localizer.nii.gz | 1 + sub-03/ses-007/anat/sub-03_ses-007_scout.json | 542 ++++++++++++++++++ .../ses-007/anat/sub-03_ses-007_scout.nii.gz | 1 + ...7_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-007_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...07_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...007_task-mario3_run-01_part-mag_events.tsv | 1 + ...007_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...07_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-01_part-phase_events.tsv | 1 + ...7_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-007_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...07_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...007_task-mario3_run-02_part-mag_events.tsv | 1 + ...007_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...07_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-02_part-phase_events.tsv | 1 + ...7_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-007_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...07_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...007_task-mario3_run-03_part-mag_events.tsv | 1 + ...007_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...07_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-03_part-phase_events.tsv | 1 + ...7_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-03/ses-007/sub-03_ses-007_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-007/anat/sub-03_ses-007_acq-axial_localizer.json create mode 120000 sub-03/ses-007/anat/sub-03_ses-007_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-007/anat/sub-03_ses-007_acq-coronal_localizer.json create mode 120000 sub-03/ses-007/anat/sub-03_ses-007_acq-coronal_localizer.nii.gz create mode 100644 sub-03/ses-007/anat/sub-03_ses-007_acq-sagittal_localizer.json create mode 120000 sub-03/ses-007/anat/sub-03_ses-007_acq-sagittal_localizer.nii.gz create mode 100644 sub-03/ses-007/anat/sub-03_ses-007_scout.json create mode 120000 sub-03/ses-007/anat/sub-03_ses-007_scout.nii.gz create mode 100644 sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 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100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 97234517f..543ce40e5 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 97234517fdca705c530d63cf0e4226503867458a +Subproject commit 543ce40e5c03216997d525b01a5de4f9033f56e6 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-03/ses-007/anat/sub-03_ses-007_acq-axial_localizer.json b/sub-03/ses-007/anat/sub-03_ses-007_acq-axial_localizer.json new file mode 100644 index 000000000..519f7196b --- /dev/null +++ b/sub-03/ses-007/anat/sub-03_ses-007_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "14:31:14.050000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + 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000000000..036432b49 --- /dev/null +++ b/sub-03/ses-007/anat/sub-03_ses-007_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "14:31:21.040000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": 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/dev/null +++ b/sub-03/ses-007/sub-03_ses-007_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/xP/Mk/MD5E-s2667--19ab70df4623637ffc7554c769c13ad8.tsv/MD5E-s2667--19ab70df4623637ffc7554c769c13ad8.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..9effe6579 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 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"%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.063618, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [626, -7221, -8773, 700, 80, 2, 26, 7], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 235.411, + "dcmmeta_affine": [ + [-1.9997897148132324, -0.013961421325802803, 0.025421932339668274, 109.18267059326172], + [-0.02016281895339489, 1.9293463230133057, -0.5265130996704102, -72.52210998535156], + [0.02084842137992382, 0.526714026927948, 1.9292842149734497, -58.11174011230469], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From cdfc6950975dd92802b5364eb89e23071cd1a363 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:09:52 -0400 Subject: [PATCH 200/463] fix fmap phase --- ...3_ses-007_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-007_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-007_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-007_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-007_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-007_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-03/ses-007/sub-03_ses-007_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-03/ses-007/fmap/{sub-03_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-007_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-007/fmap/{sub-03_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-007_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-007/fmap/{sub-03_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-007_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-007/fmap/{sub-03_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-007_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-007/fmap/{sub-03_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-007_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-007/fmap/{sub-03_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-007_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-007/fmap/{sub-03_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-007_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-007/fmap/{sub-03_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-007_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-03/ses-007/fmap/{sub-03_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-03_ses-007_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-03/ses-007/fmap/{sub-03_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-03_ses-007_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 49d755997..000000000 --- a/sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:32:15.562500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999895, 0.0100814, 0.0104242, -0.00698071, 0.964673, -0.263357], - "ImageOrientationText": "Tra>Cor(-15.3)>Sag(0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0507356, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [626, -7221, -8773, 700, 80, 2, 26, 7], - "SliceThickness": 2, - "SliceTiming": [0, 0.7825, 0.0975, 0.88, 0.195, 0.98, 0.2925, 1.0775, 0.39, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685, 0, 0.7825, 0.0975, 0.88, 0.195, 0.98, 0.2925, 1.0775, 0.39, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685, 0, 0.7825, 0.0975, 0.88, 0.195, 0.98, 0.2925, 1.0775, 0.39, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685, 0, 0.7825, 0.0975, 0.88, 0.195, 0.98, 0.2925, 1.0775, 0.39, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 235.411, - "WipMemBlock": "bbf241a7-3833-4add-9bce-d0f83a8ed97c||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9997897148132324, -0.013961421325802803, 0.025421932339668274, 109.18267059326172], - [-0.02016281895339489, 1.9293463230133057, -0.5265130996704102, -72.52210998535156], - [0.02084842137992382, 0.526714026927948, 1.9292842149734497, -58.11174011230469], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99989484497648, 0.01008140972976, 0.01042421063263, -0.006980710753, 0.96467318559069, -0.2633570099308], - "ImagePositionPatient": [-830.5861337325, -835.82191507297, 180.27488019955], - "ImageType": [ - "ORIGINAL", 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a/sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 4a523bb4d..000000000 --- a/sub-03/ses-007/fmap/sub-03_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/jq/Gk/MD5E-s3335492--57cbd81169d55b24b52a5c62bfc70281.nii.gz/MD5E-s3335492--57cbd81169d55b24b52a5c62bfc70281.nii.gz \ No newline at end of file diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 0ca6ee694..000000000 --- a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:32:5.132500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - 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1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 235.411, - "WipMemBlock": "bbf241a7-3833-4add-9bce-d0f83a8ed97c||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 068ea93e2..000000000 --- a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/PK/2Z/MD5E-s1112293--6bcba3865e29473a65611c44a655e972.nii.gz/MD5E-s1112293--6bcba3865e29473a65611c44a655e972.nii.gz \ No newline at end of file diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index fe6c88fd8..000000000 --- a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:33:36.830000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": 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"ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.063618, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 626, - -7221, - -8773, - 700, - 80, - 2, - 26, - 7 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 235.411, - "WipMemBlock": "c0807dce-ca47-4b0a-93ee-fe9f6201642b||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 9a4961481..000000000 --- a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/7f/VK/MD5E-s1103549--bd4b2329284923cc6e0c7e924dfebeb9.nii.gz/MD5E-s1103549--bd4b2329284923cc6e0c7e924dfebeb9.nii.gz \ No newline at end of file diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index b01f5f7d0..000000000 --- a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:43:57.387500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999895, - 0.0100814, - 0.0104242, - -0.00698071, - 0.964673, - -0.263357 - ], - "ImageOrientationText": "Tra>Cor(-15.3)>Sag(0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.063618, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 626, - -7221, - -8773, - 700, - 80, - 2, - 26, - 7 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 235.411, - "WipMemBlock": "534c0a0a-ca9d-4e77-b379-21aa51883c71||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index b92111c4e..000000000 --- a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Mw/mM/MD5E-s1103597--f487a955ee6e820027485ee67d457c3e.nii.gz/MD5E-s1103597--f487a955ee6e820027485ee67d457c3e.nii.gz \ No newline at end of file diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 43a56f92e..000000000 --- a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:53:57.305000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999895, - 0.0100814, - 0.0104242, - -0.00698071, - 0.964673, - -0.263357 - ], - "ImageOrientationText": "Tra>Cor(-15.3)>Sag(0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.063618, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 626, - -7221, - -8773, - 700, - 80, - 2, - 26, - 7 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 235.411, - "WipMemBlock": "fe4db19c-11e7-4970-803d-6ecc1e1401a5||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 6e0a7dae2..000000000 --- a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Pk/jW/MD5E-s1103770--0d198424875e9c9b425e896d3269d799.nii.gz/MD5E-s1103770--0d198424875e9c9b425e896d3269d799.nii.gz \ No newline at end of file diff --git a/sub-03/ses-007/sub-03_ses-007_scans.tsv b/sub-03/ses-007/sub-03_ses-007_scans.tsv index 462aa272b..0f2611083 120000 --- a/sub-03/ses-007/sub-03_ses-007_scans.tsv +++ b/sub-03/ses-007/sub-03_ses-007_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/xP/Mk/MD5E-s2667--19ab70df4623637ffc7554c769c13ad8.tsv/MD5E-s2667--19ab70df4623637ffc7554c769c13ad8.tsv \ No newline at end of file +../../.git/annex/objects/Z2/m3/MD5E-s2066--c825b71a9147291b1f8c9754fb0ce5e6.tsv/MD5E-s2066--c825b71a9147291b1f8c9754fb0ce5e6.tsv \ No newline at end of file From 5dd3839ecd802f64d34d1e49b577017e49f0c68d Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:10:00 -0400 Subject: [PATCH 201/463] fix complex event files --- ...g_events.tsv => sub-03_ses-007_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-03_ses-007_task-mario3_run-02_events.tsv} | 0 .../func/sub-03_ses-007_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-03_ses-007_task-mario3_run-03_events.tsv} | 0 .../func/sub-03_ses-007_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-03_ses-007_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-03/ses-007/func/{sub-03_ses-007_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-007_task-mario3_run-01_events.tsv} (100%) rename sub-03/ses-007/func/{sub-03_ses-007_task-mario3_run-01_part-phase_events.tsv => sub-03_ses-007_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-02_part-phase_events.tsv rename sub-03/ses-007/func/{sub-03_ses-007_task-mario3_run-02_part-mag_events.tsv => sub-03_ses-007_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-02_events.tsv similarity index 100% rename from sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-01_part-phase_events.tsv rename to sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-02_events.tsv diff --git a/sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-02_part-phase_events.tsv b/sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-02_part-mag_events.tsv b/sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-03_events.tsv similarity index 100% rename from sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-02_part-mag_events.tsv rename to sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-03_events.tsv diff --git a/sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-03_part-mag_events.tsv b/sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-03_part-phase_events.tsv b/sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-007/func/sub-03_ses-007_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 56a00ff477b347bf74240579e9dd8ef6ba00d4a1 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:10:36 -0400 Subject: [PATCH 202/463] fill IntendedFor --- ...3_ses-007_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...3_ses-007_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...3_ses-007_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...3_ses-007_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_epi.json index 489239c8a..b78abbb29 100644 --- a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999895, - 0.0100814, - 0.0104242, - -0.00698071, - 0.964673, - -0.263357 - ], + "ImageOrientationPatientDICOM": [0.999895, 0.0100814, 0.0104242, -0.00698071, 0.964673, -0.263357], "ImageOrientationText": "Tra>Cor(-15.3)>Sag(0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-03_ses-007_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-007/func/sub-03_ses-007_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-007/func/sub-03_ses-007_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 626, - -7221, - -8773, - 700, - 80, - 2, - 26, - 7 - ], + "ShimSetting": [626, -7221, -8773, 700, 80, 2, 26, 7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_epi.json b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_epi.json index ec9169982..c61b46429 100644 --- a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999895, - 0.0100814, - 0.0104242, - -0.00698071, - 0.964673, - -0.263357 - ], + "ImageOrientationPatientDICOM": [0.999895, 0.0100814, 0.0104242, -0.00698071, 0.964673, -0.263357], "ImageOrientationText": "Tra>Cor(-15.3)>Sag(0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-03_ses-007_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 626, - -7221, - -8773, - 700, - 80, - 2, - 26, - 7 - ], + "ShimSetting": [626, -7221, -8773, 700, 80, 2, 26, 7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_epi.json b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_epi.json index 8b86f8815..480a55a3d 100644 --- a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999895, - 0.0100814, - 0.0104242, - -0.00698071, - 0.964673, - -0.263357 - ], + "ImageOrientationPatientDICOM": [0.999895, 0.0100814, 0.0104242, -0.00698071, 0.964673, -0.263357], "ImageOrientationText": "Tra>Cor(-15.3)>Sag(0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-03_ses-007_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 626, - -7221, - -8773, - 700, - 80, - 2, - 26, - 7 - ], + "ShimSetting": [626, -7221, -8773, 700, 80, 2, 26, 7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_epi.json b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_epi.json index bfd70a52c..6afd3c4df 100644 --- a/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-03/ses-007/fmap/sub-03_ses-007_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999895, - 0.0100814, - 0.0104242, - -0.00698071, - 0.964673, - -0.263357 - ], + "ImageOrientationPatientDICOM": [0.999895, 0.0100814, 0.0104242, -0.00698071, 0.964673, -0.263357], "ImageOrientationText": "Tra>Cor(-15.3)>Sag(0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-03_ses-007_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 626, - -7221, - -8773, - 700, - 80, - 2, - 26, - 7 - ], + "ShimSetting": [626, -7221, -8773, 700, 80, 2, 26, 7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From d6c1632edf2681e999947470b101ab3533bd27cf Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:13:04 -0400 Subject: [PATCH 203/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..3185db2f7 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = c29963ec-a163-429c-9480-7d5fd40529b3 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..a9d93d359 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit a9d93d35925f307786dc5bb3727fa2c45935afb2 From d2acd7b97404eee2ae3374ed74cbfdc2197d78ea Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:18:52 -0400 Subject: [PATCH 204/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..2e4a49503 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 4d5bd297-8dd1-47cb-be8d-e67e1cb4daef diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..22df60cac --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 22df60cacb170a726b40372fd1f4e1b14cbba088 From cbbedef7d62e320aa2f55bfcd77f41860c59e467 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:19:11 -0400 Subject: [PATCH 205/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-004_acq-axial_localizer.json | 81 +++ .../sub-01_ses-004_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-004_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-004_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-004_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-004_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-004/anat/sub-01_ses-004_scout.json | 542 ++++++++++++++++++ .../ses-004/anat/sub-01_ses-004_scout.nii.gz | 1 + ...4_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-004_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...04_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...004_task-mario3_run-01_part-mag_events.tsv | 1 + ...004_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...04_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-01_part-phase_events.tsv | 1 + ...4_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-004_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...04_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...004_task-mario3_run-02_part-mag_events.tsv | 1 + ...004_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...04_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-02_part-phase_events.tsv | 1 + ...4_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-004_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...04_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...004_task-mario3_run-03_part-mag_events.tsv | 1 + ...004_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...04_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-03_part-phase_events.tsv | 1 + ...4_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-01/ses-004/sub-01_ses-004_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-004/anat/sub-01_ses-004_acq-axial_localizer.json create mode 120000 sub-01/ses-004/anat/sub-01_ses-004_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-004/anat/sub-01_ses-004_acq-coronal_localizer.json create mode 120000 sub-01/ses-004/anat/sub-01_ses-004_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-004/anat/sub-01_ses-004_acq-sagittal_localizer.json create mode 120000 sub-01/ses-004/anat/sub-01_ses-004_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-004/anat/sub-01_ses-004_scout.json create mode 120000 sub-01/ses-004/anat/sub-01_ses-004_scout.nii.gz create mode 100644 sub-01/ses-004/fmap/sub-01_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-004/fmap/sub-01_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-004/fmap/sub-01_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-004/fmap/sub-01_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-01/ses-004/sub-01_ses-004_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 524a17184..5ec342f24 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 524a171841aa5915e62dff159bb13b0ddd997adc +Subproject commit 5ec342f24dca9c58ee035aaa6758388a864085b5 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-004/anat/sub-01_ses-004_acq-axial_localizer.json b/sub-01/ses-004/anat/sub-01_ses-004_acq-axial_localizer.json new file mode 100644 index 000000000..083683a3d --- /dev/null +++ b/sub-01/ses-004/anat/sub-01_ses-004_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:41:4.042500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + 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+../../../.git/annex/objects/3v/jx/MD5E-s182034--a07475eda627d08b6de9b8992cf23058.nii.gz/MD5E-s182034--a07475eda627d08b6de9b8992cf23058.nii.gz \ No newline at end of file diff --git a/sub-01/ses-004/anat/sub-01_ses-004_acq-coronal_localizer.json b/sub-01/ses-004/anat/sub-01_ses-004_acq-coronal_localizer.json new file mode 100644 index 000000000..17703225c --- /dev/null +++ b/sub-01/ses-004/anat/sub-01_ses-004_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:41:11.032500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, 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"AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.995041, 0.0921747, 0.0373797, -0.0718492, 0.925962, -0.370719], + "ImageOrientationText": "Tra>Cor(-21.5)>Sag(3.9)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": 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"SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 288.112, + "dcmmeta_affine": [ + [-1.990082025527954, -0.1436983048915863, 0.13756613433361053, 109.95394897460938], + [-0.18434932827949524, 1.8519237041473389, -0.7323893308639526, -57.25645446777344], + [0.07475943118333817, 0.741437554359436, 1.8559852838516235, -64.62992858886719], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From a98e457cb858f437807e981aeb7ad59a8d1909dc Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:19:48 -0400 Subject: [PATCH 206/463] fix fmap phase --- ...1_ses-004_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-004_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-004_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-004_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-004_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-004_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-01/ses-004/sub-01_ses-004_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-01/ses-004/fmap/{sub-01_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-004_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-004/fmap/{sub-01_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-004_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-004/fmap/sub-01_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-004/fmap/sub-01_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-004/fmap/{sub-01_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-004_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-004/fmap/{sub-01_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-004_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-004/fmap/{sub-01_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-004_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-004/fmap/{sub-01_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-004_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-004/fmap/{sub-01_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-004_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-004/fmap/{sub-01_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-004_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-01/ses-004/fmap/{sub-01_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-01_ses-004_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-01/ses-004/fmap/{sub-01_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-01_ses-004_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-004/fmap/sub-01_ses-004_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-004/fmap/sub-01_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-004/fmap/sub-01_ses-004_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-004/fmap/sub-01_ses-004_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-004/fmap/sub-01_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-004/fmap/sub-01_ses-004_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-004/fmap/sub-01_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index db2c48fe1..000000000 --- a/sub-01/ses-004/fmap/sub-01_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:42:22.397500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": 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-../../../.git/annex/objects/G4/7x/MD5E-s3335218--74063f2a64d0f6744cd900aa386cc9ac.nii.gz/MD5E-s3335218--74063f2a64d0f6744cd900aa386cc9ac.nii.gz \ No newline at end of file diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 15241d0f4..000000000 --- a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:42:11.967500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 03970376c..000000000 --- a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - 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sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 0710fe723..000000000 --- a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:52:30.107500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of 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"MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0735859, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 636, - -7192, - -8813, - 654, - 108, - -9, - -21, - 3 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 288.112, - "WipMemBlock": "1ece6c53-dfd9-4627-a5c3-ba4ef914ed3d||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 15185d3a7..000000000 --- a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/M3/Pz/MD5E-s1103779--caf1299a375e330f1368bdc7004bcb5c.nii.gz/MD5E-s1103779--caf1299a375e330f1368bdc7004bcb5c.nii.gz \ No newline at end of file diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 29221f05c..000000000 --- a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:01:38.700000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995041, - 0.0921747, - 0.0373797, - -0.0718492, - 0.925962, - -0.370719 - ], - "ImageOrientationText": "Tra>Cor(-21.5)>Sag(3.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0735859, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 636, - -7192, - -8813, - 654, - 108, - -9, - -21, - 3 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 288.112, - "WipMemBlock": "4dd2436e-b169-4544-9044-4b067ed87c15||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 682cc1157..000000000 --- a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/z0/4P/MD5E-s1103768--beeaf1f8e35c60319157f807ef49ae9f.nii.gz/MD5E-s1103768--beeaf1f8e35c60319157f807ef49ae9f.nii.gz \ No newline at end of file diff --git a/sub-01/ses-004/sub-01_ses-004_scans.tsv b/sub-01/ses-004/sub-01_ses-004_scans.tsv index b8e686df6..24817efc3 120000 --- a/sub-01/ses-004/sub-01_ses-004_scans.tsv +++ b/sub-01/ses-004/sub-01_ses-004_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/7G/gF/MD5E-s2667--6891c4c95bc3403fad9fa8b4611269f9.tsv/MD5E-s2667--6891c4c95bc3403fad9fa8b4611269f9.tsv \ No newline at end of file +../../.git/annex/objects/1v/ZP/MD5E-s2066--1b475cbf52a11b0140d35e3e5cb8f55e.tsv/MD5E-s2066--1b475cbf52a11b0140d35e3e5cb8f55e.tsv \ No newline at end of file From 3094ba3ebcc4a5fbf6c7f5aad4dd43f94ed1f732 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:19:56 -0400 Subject: [PATCH 207/463] fix complex event files --- ...g_events.tsv => sub-01_ses-004_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-004_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-004_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-01_ses-004_task-mario3_run-03_events.tsv} | 0 .../func/sub-01_ses-004_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-01_ses-004_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-01/ses-004/func/{sub-01_ses-004_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-004_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-004/func/{sub-01_ses-004_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-004_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-02_part-phase_events.tsv rename sub-01/ses-004/func/{sub-01_ses-004_task-mario3_run-02_part-mag_events.tsv => sub-01_ses-004_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_events.tsv similarity index 100% rename from sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-02_part-mag_events.tsv rename to sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_events.tsv diff --git a/sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_part-mag_events.tsv b/sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-004/func/sub-01_ses-004_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 66ee3c4d05744ac5bd8d832ec4df3b27560239f0 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:20:56 -0400 Subject: [PATCH 208/463] fill IntendedFor --- ...1_ses-004_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...1_ses-004_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-004_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...1_ses-004_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_epi.json index 2504c4922..c45de839b 100644 --- a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995041, - 0.0921747, - 0.0373797, - -0.0718492, - 0.925962, - -0.370719 - ], + "ImageOrientationPatientDICOM": [0.995041, 0.0921747, 0.0373797, -0.0718492, 0.925962, -0.370719], "ImageOrientationText": "Tra>Cor(-21.5)>Sag(3.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-01_ses-004_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-004/func/sub-01_ses-004_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-004/func/sub-01_ses-004_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 636, - -7192, - -8813, - 654, - 108, - -9, - -21, - 3 - ], + "ShimSetting": [636, -7192, -8813, 654, 108, -9, -21, 3], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_epi.json index 6e56563e6..50a727d70 100644 --- a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995041, - 0.0921747, - 0.0373797, - -0.0718492, - 0.925962, - -0.370719 - ], + "ImageOrientationPatientDICOM": [0.995041, 0.0921747, 0.0373797, -0.0718492, 0.925962, -0.370719], "ImageOrientationText": "Tra>Cor(-21.5)>Sag(3.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-01_ses-004_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 636, - -7192, - -8813, - 654, - 108, - -9, - -21, - 3 - ], + "ShimSetting": [636, -7192, -8813, 654, 108, -9, -21, 3], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_epi.json index 90a1732bf..d057b4b4b 100644 --- a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995041, - 0.0921747, - 0.0373797, - -0.0718492, - 0.925962, - -0.370719 - ], + "ImageOrientationPatientDICOM": [0.995041, 0.0921747, 0.0373797, -0.0718492, 0.925962, -0.370719], "ImageOrientationText": "Tra>Cor(-21.5)>Sag(3.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-01_ses-004_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 636, - -7192, - -8813, - 654, - 108, - -9, - -21, - 3 - ], + "ShimSetting": [636, -7192, -8813, 654, 108, -9, -21, 3], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_epi.json b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_epi.json index 7e3827132..8ef70439e 100644 --- a/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-01/ses-004/fmap/sub-01_ses-004_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995041, - 0.0921747, - 0.0373797, - -0.0718492, - 0.925962, - -0.370719 - ], + "ImageOrientationPatientDICOM": [0.995041, 0.0921747, 0.0373797, -0.0718492, 0.925962, -0.370719], "ImageOrientationText": "Tra>Cor(-21.5)>Sag(3.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-01_ses-004_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 636, - -7192, - -8813, - 654, - 108, - -9, - -21, - 3 - ], + "ShimSetting": [636, -7192, -8813, 654, 108, -9, -21, 3], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 3a206e706f33c7af1f5ce5a9bae559f81b4f9e74 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:21:45 -0400 Subject: [PATCH 209/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..fe9dc4ffe --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 0be4438a-3626-4dc8-bb64-7a34c38ac2ce diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..b2f5f6097 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit b2f5f6097e6be93eaeb37ca48a0806a853f0c927 From 6e8ef01a50460e6e09984089f8ce8f45ac158583 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:22:06 -0400 Subject: [PATCH 210/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..c433c437a --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 5fd9d6cb-7e95-4141-8c1c-ca20152b87c4 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..552c22800 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 552c22800cfc34b219530810f83f7443fd5e227f From efb631ad774b05c9aa32140324ea31aa6bde8fba Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:22:32 -0400 Subject: [PATCH 211/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-03_ses-009_acq-axial_localizer.json | 81 +++ .../sub-03_ses-009_acq-axial_localizer.nii.gz | 1 + .../sub-03_ses-009_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-009_acq-coronal_localizer.nii.gz | 1 + ...sub-03_ses-009_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-009_acq-sagittal_localizer.nii.gz | 1 + sub-03/ses-009/anat/sub-03_ses-009_scout.json | 542 ++++++++++++++++++ .../ses-009/anat/sub-03_ses-009_scout.nii.gz | 1 + ...9_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-009_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...09_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...009_task-mario3_run-01_part-mag_events.tsv | 1 + ...009_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...09_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-01_part-phase_events.tsv | 1 + ...9_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-009_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...09_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...009_task-mario3_run-02_part-mag_events.tsv | 1 + ...009_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...09_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-02_part-phase_events.tsv | 1 + ...9_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-009_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...09_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...009_task-mario3_run-03_part-mag_events.tsv | 1 + ...009_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...09_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-03_part-phase_events.tsv | 1 + ...9_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-03/ses-009/sub-03_ses-009_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-009/anat/sub-03_ses-009_acq-axial_localizer.json create mode 120000 sub-03/ses-009/anat/sub-03_ses-009_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-009/anat/sub-03_ses-009_acq-coronal_localizer.json create mode 120000 sub-03/ses-009/anat/sub-03_ses-009_acq-coronal_localizer.nii.gz create mode 100644 sub-03/ses-009/anat/sub-03_ses-009_acq-sagittal_localizer.json create mode 120000 sub-03/ses-009/anat/sub-03_ses-009_acq-sagittal_localizer.nii.gz create mode 100644 sub-03/ses-009/anat/sub-03_ses-009_scout.json create mode 120000 sub-03/ses-009/anat/sub-03_ses-009_scout.nii.gz create mode 100644 sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-02_part-mag_events.tsv create mode 100644 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a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-03/ses-009/anat/sub-03_ses-009_acq-axial_localizer.json b/sub-03/ses-009/anat/sub-03_ses-009_acq-axial_localizer.json new file mode 100644 index 000000000..b5c08a361 --- /dev/null +++ b/sub-03/ses-009/anat/sub-03_ses-009_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "13:59:33.050000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + 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"http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999471, 0.00107425, 0.0324964, 0.00837337, 0.957238, -0.289179], + "ImageOrientationText": "Tra>Cor(-16.8)>Sag(1.8)", + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": 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240.994, + "dcmmeta_affine": [ + [-1.998942494392395, 0.016746746376156807, 0.06283489614725113, 106.6191177368164], + [-0.002148508792743087, 1.914476990699768, -0.5785958170890808, -71.8367691040039], + [0.06499277800321579, 0.5783573985099792, 1.9134467840194702, -55.003440856933594], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 5786dcc09a3b719af2675ddca7e9dc612bf16e65 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:23:07 -0400 Subject: [PATCH 212/463] fix fmap phase --- ...3_ses-009_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-009_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-009_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-009_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-009_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-009_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-03/ses-009/sub-03_ses-009_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-03/ses-009/fmap/{sub-03_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-009_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-009/fmap/{sub-03_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-009_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-009/fmap/{sub-03_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-009_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-009/fmap/{sub-03_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-009_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-009/fmap/{sub-03_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-009_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-009/fmap/{sub-03_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-009_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-009/fmap/{sub-03_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-009_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-009/fmap/{sub-03_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-009_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-03/ses-009/fmap/{sub-03_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-03_ses-009_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-03/ses-009/fmap/{sub-03_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-03_ses-009_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 1a642779f..000000000 --- a/sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:00:35.190000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999471, 0.00107425, 0.0324964, 0.00837337, 0.957238, -0.289179], - "ImageOrientationText": "Tra>Cor(-16.8)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0523143, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [639, -7219, -8747, 658, 89, 4, 6, 5], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 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"slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["140035.190000", "140036.680000", "140038.170000"], - "ContentTime": ["140121.392000", "140121.416000", "140121.418000"], - "InstanceCreationTime": ["140121.392000", "140121.416000", "140121.418000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4856.0, 4856.0, 4858.0], - "WindowWidth": [18606.0, 18604.0, 18612.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 20f14ee16..000000000 --- a/sub-03/ses-009/fmap/sub-03_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/51/8V/MD5E-s3335259--ee2f5870f6dfc09d8e5cbb21acbddb75.nii.gz/MD5E-s3335259--ee2f5870f6dfc09d8e5cbb21acbddb75.nii.gz \ No newline at end of file diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 5414799e4..000000000 --- a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:00:24.760000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999471, - 0.00107425, - 0.0324964, - 0.00837337, - 0.957238, - -0.289179 - ], - "ImageOrientationText": 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"TotalReadoutTime": 0.0576811, - "TxRefAmp": 240.994, - "WipMemBlock": "35e3dc7d-46e8-4e48-b979-e81a6ccc693a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index f4e71a495..000000000 --- a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/JW/9q/MD5E-s1112447--8e8dcd86a07b7d622cddd9df5d090758.nii.gz/MD5E-s1112447--8e8dcd86a07b7d622cddd9df5d090758.nii.gz \ No newline at end of file diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index e6d064b43..000000000 --- a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:02:19.710000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": 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"SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 240.994, - "WipMemBlock": "4f61f681-4036-4fee-be43-299f3b5c041f||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 6b221030c..000000000 --- a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/v9/mz/MD5E-s1103642--f57fa8adeaccfc64afe9a5d50cc9b27d.nii.gz/MD5E-s1103642--f57fa8adeaccfc64afe9a5d50cc9b27d.nii.gz \ No newline at end of file diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 49e248b3c..000000000 --- a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:13:50.337500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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"PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0655975, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 639, - -7219, - -8747, - 658, - 89, - 4, - 6, - 5 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 240.994, - "WipMemBlock": "b35539bb-fbd9-4227-b655-dce674fd88b1||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 97fc0ad5f..000000000 --- a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/fM/p5/MD5E-s1103762--7f67e1b90879bdf3cbd7300af72a2713.nii.gz/MD5E-s1103762--7f67e1b90879bdf3cbd7300af72a2713.nii.gz \ No newline at end of file diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index f49f9439c..000000000 --- a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:26:12.630000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999471, - 0.00107425, - 0.0324964, - 0.00837337, - 0.957238, - -0.289179 - ], - "ImageOrientationText": "Tra>Cor(-16.8)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0655975, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 639, - -7219, - -8747, - 658, - 89, - 4, - 6, - 5 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 240.994, - "WipMemBlock": "0a857153-81bb-481a-bd28-d03ff9119183||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index dd26331f4..000000000 --- a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/wz/gw/MD5E-s1103629--179b7d59d22d14da07d4b899cf16b4eb.nii.gz/MD5E-s1103629--179b7d59d22d14da07d4b899cf16b4eb.nii.gz \ No newline at end of file diff --git a/sub-03/ses-009/sub-03_ses-009_scans.tsv b/sub-03/ses-009/sub-03_ses-009_scans.tsv index 09f32c0cc..4347f741d 120000 --- a/sub-03/ses-009/sub-03_ses-009_scans.tsv +++ b/sub-03/ses-009/sub-03_ses-009_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/J2/V3/MD5E-s2667--fc0c6c4c9410e86f0dc780c6a5defa52.tsv/MD5E-s2667--fc0c6c4c9410e86f0dc780c6a5defa52.tsv \ No newline at end of file +../../.git/annex/objects/7K/41/MD5E-s2066--0dc69bb6ee1096417ace934a53edd916.tsv/MD5E-s2066--0dc69bb6ee1096417ace934a53edd916.tsv \ No newline at end of file From 022905bdf2abe98c950c1f0d2f30fd99827c8b55 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:23:16 -0400 Subject: [PATCH 213/463] fix complex event files --- ...g_events.tsv => sub-03_ses-009_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-03_ses-009_task-mario3_run-02_events.tsv} | 0 .../func/sub-03_ses-009_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-03_ses-009_task-mario3_run-03_events.tsv} | 0 .../func/sub-03_ses-009_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-03_ses-009_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-03/ses-009/func/{sub-03_ses-009_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-009_task-mario3_run-01_events.tsv} (100%) rename sub-03/ses-009/func/{sub-03_ses-009_task-mario3_run-01_part-phase_events.tsv => sub-03_ses-009_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-02_part-phase_events.tsv rename sub-03/ses-009/func/{sub-03_ses-009_task-mario3_run-02_part-mag_events.tsv => sub-03_ses-009_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-02_events.tsv similarity index 100% rename from sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-01_part-phase_events.tsv rename to sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-02_events.tsv diff --git a/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-02_part-phase_events.tsv b/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-02_part-mag_events.tsv b/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-03_events.tsv similarity index 100% rename from sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-02_part-mag_events.tsv rename to sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-03_events.tsv diff --git a/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-03_part-mag_events.tsv b/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-03_part-phase_events.tsv b/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From a570246d9f1fc5570d1feee441207d9998c2c359 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:24:16 -0400 Subject: [PATCH 214/463] fill IntendedFor --- ...3_ses-009_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...3_ses-009_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...3_ses-009_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...3_ses-009_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_epi.json index 673a367c3..2a3c5544f 100644 --- a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999471, - 0.00107425, - 0.0324964, - 0.00837337, - 0.957238, - -0.289179 - ], + "ImageOrientationPatientDICOM": [0.999471, 0.00107425, 0.0324964, 0.00837337, 0.957238, -0.289179], "ImageOrientationText": "Tra>Cor(-16.8)>Sag(1.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-009/func/sub-03_ses-009_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-009/func/sub-03_ses-009_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-009/func/sub-03_ses-009_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 639, - -7219, - -8747, - 658, - 89, - 4, - 6, - 5 - ], + "ShimSetting": [639, -7219, -8747, 658, 89, 4, 6, 5], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_epi.json b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_epi.json index f7c6aaa07..11db6cdcf 100644 --- a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999471, - 0.00107425, - 0.0324964, - 0.00837337, - 0.957238, - -0.289179 - ], + "ImageOrientationPatientDICOM": [0.999471, 0.00107425, 0.0324964, 0.00837337, 0.957238, -0.289179], "ImageOrientationText": "Tra>Cor(-16.8)>Sag(1.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-009/func/sub-03_ses-009_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 639, - -7219, - -8747, - 658, - 89, - 4, - 6, - 5 - ], + "ShimSetting": [639, -7219, -8747, 658, 89, 4, 6, 5], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_epi.json b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_epi.json index 74d0d46bc..132876cb8 100644 --- a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999471, - 0.00107425, - 0.0324964, - 0.00837337, - 0.957238, - -0.289179 - ], + "ImageOrientationPatientDICOM": [0.999471, 0.00107425, 0.0324964, 0.00837337, 0.957238, -0.289179], "ImageOrientationText": "Tra>Cor(-16.8)>Sag(1.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-009/func/sub-03_ses-009_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 639, - -7219, - -8747, - 658, - 89, - 4, - 6, - 5 - ], + "ShimSetting": [639, -7219, -8747, 658, 89, 4, 6, 5], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_epi.json b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_epi.json index fca1234fa..6b755686f 100644 --- a/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-03/ses-009/fmap/sub-03_ses-009_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999471, - 0.00107425, - 0.0324964, - 0.00837337, - 0.957238, - -0.289179 - ], + "ImageOrientationPatientDICOM": [0.999471, 0.00107425, 0.0324964, 0.00837337, 0.957238, -0.289179], "ImageOrientationText": "Tra>Cor(-16.8)>Sag(1.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-009/func/sub-03_ses-009_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 639, - -7219, - -8747, - 658, - 89, - 4, - 6, - 5 - ], + "ShimSetting": [639, -7219, -8747, 658, 89, 4, 6, 5], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.4875, 0.5875, 0.685, 0.7825, 0.88, 0.9775, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.485, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 976337a17358e3255967c0cd9b9dfcd7d2cf2a80 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:24:52 -0400 Subject: [PATCH 215/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..f7effc979 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 4475a867-9bc4-4466-982d-9733a0c42048 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..8ca46063f --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 8ca46063fec6649bd95d4fdd38c7eb2fc4c3c5c0 From 08d1cc840972b048760bd8216b8c25eff60370ae Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:25:10 -0400 Subject: [PATCH 216/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..dacea1c1e --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = f3566441-4931-44f8-bb19-ce136365dde9 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..8f495782a --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 8f495782a70b9cc5331d47833247d080de7276fa From ca6d550e6b72d8138e3ebd7b3a554e96bdb55996 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:25:16 -0400 Subject: [PATCH 217/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-03_ses-013_acq-axial_localizer.json | 81 +++ .../sub-03_ses-013_acq-axial_localizer.nii.gz | 1 + .../sub-03_ses-013_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-013_acq-coronal_localizer.nii.gz | 1 + ...sub-03_ses-013_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-013_acq-sagittal_localizer.nii.gz | 1 + sub-03/ses-013/anat/sub-03_ses-013_scout.json | 542 ++++++++++++++++++ .../ses-013/anat/sub-03_ses-013_scout.nii.gz | 1 + ...3_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-013_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...13_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...013_task-mario3_run-01_part-mag_events.tsv | 1 + ...013_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...13_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-01_part-phase_events.tsv | 1 + ...3_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-013_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...13_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...013_task-mario3_run-02_part-mag_events.tsv | 1 + ...013_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...13_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-02_part-phase_events.tsv | 1 + ...3_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-013_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...13_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...013_task-mario3_run-03_part-mag_events.tsv | 1 + ...013_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...13_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-03_part-phase_events.tsv | 1 + ...3_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-013_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...13_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...013_task-mario3_run-04_part-mag_events.tsv | 1 + ...013_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...13_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-04_part-phase_events.tsv | 1 + ...3_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-03/ses-013/sub-03_ses-013_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5409 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-013/anat/sub-03_ses-013_acq-axial_localizer.json create mode 120000 sub-03/ses-013/anat/sub-03_ses-013_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-013/anat/sub-03_ses-013_acq-coronal_localizer.json create mode 120000 sub-03/ses-013/anat/sub-03_ses-013_acq-coronal_localizer.nii.gz create mode 100644 sub-03/ses-013/anat/sub-03_ses-013_acq-sagittal_localizer.json create mode 120000 sub-03/ses-013/anat/sub-03_ses-013_acq-sagittal_localizer.nii.gz create mode 100644 sub-03/ses-013/anat/sub-03_ses-013_scout.json create mode 120000 sub-03/ses-013/anat/sub-03_ses-013_scout.nii.gz create mode 100644 sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 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participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-03/ses-013/anat/sub-03_ses-013_acq-axial_localizer.json b/sub-03/ses-013/anat/sub-03_ses-013_acq-axial_localizer.json new file mode 100644 index 000000000..42dc968b6 --- /dev/null +++ b/sub-03/ses-013/anat/sub-03_ses-013_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:11:43.057500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + 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b/sub-03/ses-013/anat/sub-03_ses-013_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..5ddb1c9d2 --- /dev/null +++ b/sub-03/ses-013/anat/sub-03_ses-013_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/9G/GM/MD5E-s161510--7eb4e73cf26d274c39b79c05b0423654.nii.gz/MD5E-s161510--7eb4e73cf26d274c39b79c05b0423654.nii.gz \ No newline at end of file diff --git a/sub-03/ses-013/anat/sub-03_ses-013_acq-coronal_localizer.json b/sub-03/ses-013/anat/sub-03_ses-013_acq-coronal_localizer.json new file mode 100644 index 000000000..5189b2f8a --- /dev/null +++ b/sub-03/ses-013/anat/sub-03_ses-013_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:11:50.047500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", 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+../../../.git/annex/objects/55/W7/MD5E-s185535--33cb5b026e622dd974096c87c469dac4.nii.gz/MD5E-s185535--33cb5b026e622dd974096c87c469dac4.nii.gz \ No newline at end of file diff --git a/sub-03/ses-013/anat/sub-03_ses-013_acq-sagittal_localizer.json b/sub-03/ses-013/anat/sub-03_ses-013_acq-sagittal_localizer.json new file mode 100644 index 000000000..34a5b95a7 --- /dev/null +++ b/sub-03/ses-013/anat/sub-03_ses-013_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:11:36.067500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 0, + 1, + 0, + 0, + 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index 000000000..1bbdfddb5 --- /dev/null +++ b/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-04_part-phase_events.tsv @@ -0,0 +1 @@ +../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-04_part-phase_sbref.json b/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-04_part-phase_sbref.json new file mode 100644 index 000000000..19edeaadd --- /dev/null +++ b/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-04_part-phase_sbref.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:39:16.592500", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + 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"http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999875, 0.0112852, 0.0110576, -0.00820223, 0.968932, -0.247192], + "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.8)", + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0362188, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [621, -7242, -8716, 737, 63, -41, 79, 6], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 206.33, + "dcmmeta_affine": [ + [-1.9997503757476807, -0.01640445552766323, 0.027007432654500008, 109.14628601074219], + [-0.02257036231458187, 1.9378634691238403, -0.4941416382789612, -73.79918670654297], + [0.022115295752882957, 0.4943847358226776, 1.9378067255020142, -38.52891540527344], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 92da4998e6b5139a737745a61fc5de17b86a1cbd Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:25:49 -0400 Subject: [PATCH 218/463] fix fmap phase --- ...3_ses-013_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-013_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-013_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-013_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-013_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-013_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-013_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-013_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-013_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-013_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-013_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-013_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-03/ses-013/sub-03_ses-013_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-03/ses-013/fmap/{sub-03_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-013_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-013/fmap/{sub-03_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-013_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-013/fmap/{sub-03_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-013_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-013/fmap/{sub-03_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-013_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-013/fmap/{sub-03_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-013_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-013/fmap/{sub-03_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-013_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-013/fmap/{sub-03_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-013_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-013/fmap/{sub-03_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-013_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-03/ses-013/fmap/{sub-03_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-03_ses-013_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-03/ses-013/fmap/{sub-03_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-03_ses-013_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-03/ses-013/fmap/{sub-03_ses-013_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-03_ses-013_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-03/ses-013/fmap/{sub-03_ses-013_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-03_ses-013_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 3696a048d..000000000 --- a/sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:12:49.962500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - 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- "ImageOrientationPatient": [0.99987517876512, 0.0112851811111, 0.01105764788283, -0.0082022274594, 0.96893170883032, -0.2471923685874], - "ImagePositionPatient": [-829.39453256747, -839.39863915307, 184.29879107167], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.260261, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "181057.394000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.02888463766302, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "181336.796000", - "SliceLocation": -17.623286338467, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000361748, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "181057.315000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["181249.962500", "181251.452500", "181252.942500"], - "ContentTime": ["181336.798000", "181336.801000", "181336.804000"], - "InstanceCreationTime": ["181336.798000", "181336.801000", "181336.804000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4868.0, 4866.0, 4870.0], - "WindowWidth": [18678.0, 18674.0, 18678.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 7555e4a5e..000000000 --- a/sub-03/ses-013/fmap/sub-03_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/66/KV/MD5E-s3334397--1e84cb26172a8ed8e6b4c91277c5b5f8.nii.gz/MD5E-s3334397--1e84cb26172a8ed8e6b4c91277c5b5f8.nii.gz \ No newline at end of file diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 557a9e8e6..000000000 --- a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:12:39.532500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999875, - 0.0112852, - 0.0110576, - -0.00820223, - 0.968932, - -0.247192 - ], - "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0288846, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 621, - -7242, - -8716, - 737, - 63, - -41, - 79, - 6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 206.33, - "WipMemBlock": "a8376ac8-368f-4739-8332-29716113f82c||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index e45ccf34f..000000000 --- a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/mw/Vg/MD5E-s1112482--ad91d2d886b357f4b5678402a50bccad.nii.gz/MD5E-s1112482--ad91d2d886b357f4b5678402a50bccad.nii.gz \ No newline at end of file diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 4a272b4cc..000000000 --- a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:13:42.252500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999875, - 0.0112852, - 0.0110576, - -0.00820223, - 0.968932, - -0.247192 - ], - "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0362188, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 621, - -7242, - -8716, - 737, - 63, - -41, - 79, - 6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 206.33, - "WipMemBlock": "875ac3a8-6dea-4355-9c52-660a37b03156||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 1bbdc789b..000000000 --- a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/pV/jk/MD5E-s1103678--882c09897193484b6546554c6290b574.nii.gz/MD5E-s1103678--882c09897193484b6546554c6290b574.nii.gz \ No newline at end of file diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index e146fdfec..000000000 --- a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:21:48.095000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999875, - 0.0112852, - 0.0110576, - -0.00820223, - 0.968932, - -0.247192 - ], - "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0362188, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 621, - -7242, - -8716, - 737, - 63, - -41, - 79, - 6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 206.33, - "WipMemBlock": "577e49d7-3de4-4e39-8331-e73ecd87c319||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 35bcd69ff..000000000 --- a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Mx/2v/MD5E-s1103810--2edeac2e7ca1edb55919fec3ab1210e5.nii.gz/MD5E-s1103810--2edeac2e7ca1edb55919fec3ab1210e5.nii.gz \ No newline at end of file diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 48e3f6b04..000000000 --- a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:30:28.412500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999875, - 0.0112852, - 0.0110576, - -0.00820223, - 0.968932, - -0.247192 - ], - "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0362188, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 621, - -7242, - -8716, - 737, - 63, - -41, - 79, - 6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 206.33, - "WipMemBlock": "022883d4-2e90-415b-b460-212d92f25562||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index a08944ed4..000000000 --- a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/G8/1Z/MD5E-s1103746--607a012ccf4ad0a32dbdbf868adc7b56.nii.gz/MD5E-s1103746--607a012ccf4ad0a32dbdbf868adc7b56.nii.gz \ No newline at end of file diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 1caac676c..000000000 --- a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:39:16.592500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999875, - 0.0112852, - 0.0110576, - -0.00820223, - 0.968932, - -0.247192 - ], - "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0362188, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 621, - -7242, - -8716, - 737, - 63, - -41, - 79, - 6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 206.33, - "WipMemBlock": "75b8104b-8dad-43bc-8356-9387539d15ef||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 6893f7fae..000000000 --- a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/qP/jK/MD5E-s1103792--430d849dda7792e76a8b21b5ca6228dc.nii.gz/MD5E-s1103792--430d849dda7792e76a8b21b5ca6228dc.nii.gz \ No newline at end of file diff --git a/sub-03/ses-013/sub-03_ses-013_scans.tsv b/sub-03/ses-013/sub-03_ses-013_scans.tsv index f6bde3403..b45aa86a8 120000 --- a/sub-03/ses-013/sub-03_ses-013_scans.tsv +++ b/sub-03/ses-013/sub-03_ses-013_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/xJ/Xf/MD5E-s3289--8de02f387ad68629007b7bab8ba9addc.tsv/MD5E-s3289--8de02f387ad68629007b7bab8ba9addc.tsv \ No newline at end of file +../../.git/annex/objects/W6/x8/MD5E-s2567--51ad08ff52cda52d1cfdc6d989692884.tsv/MD5E-s2567--51ad08ff52cda52d1cfdc6d989692884.tsv \ No newline at end of file From 93d2dcef16fe0842990f9f6d12eba9bfc1d2d3d0 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:25:58 -0400 Subject: [PATCH 219/463] fix complex event files --- ...g_events.tsv => sub-03_ses-013_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-03_ses-013_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-03_ses-013_task-mario3_run-03_events.tsv} | 0 .../func/sub-03_ses-013_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-03_ses-013_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-03_ses-013_task-mario3_run-04_events.tsv} | 0 .../func/sub-03_ses-013_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-03_ses-013_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-03/ses-013/func/{sub-03_ses-013_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-013_task-mario3_run-01_events.tsv} (100%) rename sub-03/ses-013/func/{sub-03_ses-013_task-mario3_run-01_part-phase_events.tsv => sub-03_ses-013_task-mario3_run-02_events.tsv} (100%) rename sub-03/ses-013/func/{sub-03_ses-013_task-mario3_run-02_part-mag_events.tsv => sub-03_ses-013_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-03_part-phase_events.tsv rename sub-03/ses-013/func/{sub-03_ses-013_task-mario3_run-02_part-phase_events.tsv => sub-03_ses-013_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-02_events.tsv similarity index 100% rename from sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-01_part-phase_events.tsv rename to sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-02_events.tsv diff --git a/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-02_part-mag_events.tsv b/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-03_events.tsv similarity index 100% rename from sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-02_part-mag_events.tsv rename to sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-03_events.tsv diff --git a/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-03_part-mag_events.tsv b/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-03_part-phase_events.tsv b/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-02_part-phase_events.tsv b/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-04_events.tsv similarity index 100% rename from sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-02_part-phase_events.tsv rename to sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-04_events.tsv diff --git a/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-04_part-mag_events.tsv b/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-04_part-phase_events.tsv b/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-013/func/sub-03_ses-013_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From b6c31c4e8c23a3ddb60f56eb799c8d57ee781ed7 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:26:51 -0400 Subject: [PATCH 220/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..736b4a8d0 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = a0a06340-9c5b-49ff-8295-8be9075b9e32 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..d6ec7f6be --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit d6ec7f6be23a662834cc01e70720430f1d6fdd3d From 29a0351cbb462640dc26c30b343b8366be4b14c8 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:27:09 -0400 Subject: [PATCH 221/463] fill IntendedFor --- ...3_ses-013_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...3_ses-013_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...3_ses-013_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...3_ses-013_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...3_ses-013_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_epi.json index a03999049..51a8ba06a 100644 --- a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999875, - 0.0112852, - 0.0110576, - -0.00820223, - 0.968932, - -0.247192 - ], + "ImageOrientationPatientDICOM": [0.999875, 0.0112852, 0.0110576, -0.00820223, 0.968932, -0.247192], "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-013/func/sub-03_ses-013_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-013/func/sub-03_ses-013_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-013/func/sub-03_ses-013_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-013/func/sub-03_ses-013_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 621, - -7242, - -8716, - 737, - 63, - -41, - 79, - 6 - ], + "ShimSetting": [621, -7242, -8716, 737, 63, -41, 79, 6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.02, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_epi.json b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_epi.json index c54da2555..45c2b5db6 100644 --- a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999875, - 0.0112852, - 0.0110576, - -0.00820223, - 0.968932, - -0.247192 - ], + "ImageOrientationPatientDICOM": [0.999875, 0.0112852, 0.0110576, -0.00820223, 0.968932, -0.247192], "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-013/func/sub-03_ses-013_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 621, - -7242, - -8716, - 737, - 63, - -41, - 79, - 6 - ], + "ShimSetting": [621, -7242, -8716, 737, 63, -41, 79, 6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_epi.json b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_epi.json index 367184075..f01d35c2d 100644 --- a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999875, - 0.0112852, - 0.0110576, - -0.00820223, - 0.968932, - -0.247192 - ], + "ImageOrientationPatientDICOM": [0.999875, 0.0112852, 0.0110576, -0.00820223, 0.968932, -0.247192], "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-013/func/sub-03_ses-013_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 621, - -7242, - -8716, - 737, - 63, - -41, - 79, - 6 - ], + "ShimSetting": [621, -7242, -8716, 737, 63, -41, 79, 6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_epi.json b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_epi.json index b1d7188d3..906609b46 100644 --- a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999875, - 0.0112852, - 0.0110576, - -0.00820223, - 0.968932, - -0.247192 - ], + "ImageOrientationPatientDICOM": [0.999875, 0.0112852, 0.0110576, -0.00820223, 0.968932, -0.247192], "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-013/func/sub-03_ses-013_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 621, - -7242, - -8716, - 737, - 63, - -41, - 79, - 6 - ], + "ShimSetting": [621, -7242, -8716, 737, 63, -41, 79, 6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_epi.json b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_epi.json index 16d991017..81818652c 100644 --- a/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-03/ses-013/fmap/sub-03_ses-013_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999875, - 0.0112852, - 0.0110576, - -0.00820223, - 0.968932, - -0.247192 - ], + "ImageOrientationPatientDICOM": [0.999875, 0.0112852, 0.0110576, -0.00820223, 0.968932, -0.247192], "ImageOrientationText": "Tra>Cor(-14.3)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-013/func/sub-03_ses-013_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 621, - -7242, - -8716, - 737, - 63, - -41, - 79, - 6 - ], + "ShimSetting": [621, -7242, -8716, 737, 63, -41, 79, 6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 5fcf78ecb2491dadd194554b64440592fb85f923 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:27:22 -0400 Subject: [PATCH 222/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-05_ses-005_acq-axial_localizer.json | 81 +++ .../sub-05_ses-005_acq-axial_localizer.nii.gz | 1 + .../sub-05_ses-005_acq-coronal_localizer.json | 81 +++ ...ub-05_ses-005_acq-coronal_localizer.nii.gz | 1 + ...sub-05_ses-005_acq-sagittal_localizer.json | 86 +++ ...b-05_ses-005_acq-sagittal_localizer.nii.gz | 1 + sub-05/ses-005/anat/sub-05_ses-005_scout.json | 671 ++++++++++++++++++ .../ses-005/anat/sub-05_ses-005_scout.nii.gz | 1 + ...5_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 +++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 +++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 ++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 ++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 ++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 ++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 ++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 ++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 ++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 ++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 ++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 ++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-005_task-mario3_run-01_part-mag_bold.json | 172 +++++ ...05_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...005_task-mario3_run-01_part-mag_events.tsv | 1 + ...005_task-mario3_run-01_part-mag_sbref.json | 150 ++++ ...5_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...05_task-mario3_run-01_part-phase_bold.json | 178 +++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-01_part-phase_events.tsv | 1 + ...5_task-mario3_run-01_part-phase_sbref.json | 153 ++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-005_task-mario3_run-02_part-mag_bold.json | 172 +++++ ...05_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...005_task-mario3_run-02_part-mag_events.tsv | 1 + ...005_task-mario3_run-02_part-mag_sbref.json | 150 ++++ ...5_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...05_task-mario3_run-02_part-phase_bold.json | 178 +++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-02_part-phase_events.tsv | 1 + ...5_task-mario3_run-02_part-phase_sbref.json | 153 ++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-005_task-mario3_run-03_part-mag_bold.json | 172 +++++ ...05_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...005_task-mario3_run-03_part-mag_events.tsv | 1 + ...005_task-mario3_run-03_part-mag_sbref.json | 150 ++++ ...5_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...05_task-mario3_run-03_part-phase_bold.json | 178 +++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-03_part-phase_events.tsv | 1 + ...5_task-mario3_run-03_part-phase_sbref.json | 153 ++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-005_task-mario3_run-04_part-mag_bold.json | 172 +++++ ...05_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...005_task-mario3_run-04_part-mag_events.tsv | 1 + ...005_task-mario3_run-04_part-mag_sbref.json | 150 ++++ ...5_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...05_task-mario3_run-04_part-phase_bold.json | 178 +++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-04_part-phase_events.tsv | 1 + ...5_task-mario3_run-04_part-phase_sbref.json | 153 ++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-05/ses-005/sub-05_ses-005_scans.tsv | 1 + task-mario3_bold.json | 75 ++ 79 files changed, 5538 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-05/ses-005/anat/sub-05_ses-005_acq-axial_localizer.json create mode 120000 sub-05/ses-005/anat/sub-05_ses-005_acq-axial_localizer.nii.gz create mode 100644 sub-05/ses-005/anat/sub-05_ses-005_acq-coronal_localizer.json create mode 120000 sub-05/ses-005/anat/sub-05_ses-005_acq-coronal_localizer.nii.gz create mode 100644 sub-05/ses-005/anat/sub-05_ses-005_acq-sagittal_localizer.json create mode 120000 sub-05/ses-005/anat/sub-05_ses-005_acq-sagittal_localizer.nii.gz create mode 100644 sub-05/ses-005/anat/sub-05_ses-005_scout.json create mode 120000 sub-05/ses-005/anat/sub-05_ses-005_scout.nii.gz create mode 100644 sub-05/ses-005/fmap/sub-05_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-05/ses-005/fmap/sub-05_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-005/fmap/sub-05_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-05/ses-005/fmap/sub-05_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-02_part-phase_bold.json create mode 120000 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sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_part-phase_sbref.nii.gz create mode 120000 sub-05/ses-005/sub-05_ses-005_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index d6ec7f6be..f372eaade 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit d6ec7f6be23a662834cc01e70720430f1d6fdd3d +Subproject commit f372eaadeb09751be7220dc7313af462bb84c60b diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..da8d4ae9f --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-05 50 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-05/ses-005/anat/sub-05_ses-005_acq-axial_localizer.json b/sub-05/ses-005/anat/sub-05_ses-005_acq-axial_localizer.json new file mode 100644 index 000000000..1d2b44dc6 --- /dev/null +++ b/sub-05/ses-005/anat/sub-05_ses-005_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "19:03:14.057500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + 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000000000..4c77ef6b5 --- /dev/null +++ b/sub-05/ses-005/anat/sub-05_ses-005_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/5m/W2/MD5E-s176912--b203b95bb9d06fc525d7bf1c7c9a9fa9.nii.gz/MD5E-s176912--b203b95bb9d06fc525d7bf1c7c9a9fa9.nii.gz \ No newline at end of file diff --git a/sub-05/ses-005/anat/sub-05_ses-005_acq-coronal_localizer.json b/sub-05/ses-005/anat/sub-05_ses-005_acq-coronal_localizer.json new file mode 100644 index 000000000..a00d1ccab --- /dev/null +++ b/sub-05/ses-005/anat/sub-05_ses-005_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "19:03:21.047500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + 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0.6} \ No newline at end of file From 6af757590c24ff1edd06106ee9d44929226177ec Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:28:07 -0400 Subject: [PATCH 223/463] fix fmap phase --- ...5_ses-005_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-005_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-005_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-005_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-005_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-005_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-005_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-05/ses-005/sub-05_ses-005_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-05/ses-005/fmap/{sub-05_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-05_ses-005_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-005/fmap/{sub-05_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-005_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-005/fmap/sub-05_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-005/fmap/sub-05_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-005/fmap/{sub-05_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-05_ses-005_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-005/fmap/{sub-05_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-005_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-005/fmap/{sub-05_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-05_ses-005_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-05/ses-005/fmap/{sub-05_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-05_ses-005_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-05/ses-005/fmap/{sub-05_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-05_ses-005_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-05/ses-005/fmap/{sub-05_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-05_ses-005_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-05/ses-005/fmap/{sub-05_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-05_ses-005_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-05/ses-005/fmap/{sub-05_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-05_ses-005_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-05/ses-005/fmap/{sub-05_ses-005_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-05_ses-005_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-05/ses-005/fmap/{sub-05_ses-005_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-05_ses-005_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-005/fmap/sub-05_ses-005_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-005/fmap/sub-05_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-005/fmap/sub-05_ses-005_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-005/fmap/sub-05_ses-005_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-005/fmap/sub-05_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-005/fmap/sub-05_ses-005_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-005/fmap/sub-05_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 83a23e14a..000000000 --- a/sub-05/ses-005/fmap/sub-05_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:05:21.197500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", 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a/sub-05/ses-005/fmap/sub-05_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/gk/1J/MD5E-s3333970--c1ef6c7f6570661f4fb9cd71b4f874bc.nii.gz/MD5E-s3333970--c1ef6c7f6570661f4fb9cd71b4f874bc.nii.gz \ No newline at end of file diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index b88602c99..000000000 --- a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:05:10.767500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": 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- "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0579163, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 589, - -7297, - -8821, - 389, - 47, - -370, - -32, - 109 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 286.202, - "WipMemBlock": "21681ad6-2c69-424b-a4c0-17a7085eac88||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index b969a8906..000000000 --- a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/mq/3z/MD5E-s1111998--c65e9e57fad097d581c969964001670f.nii.gz/MD5E-s1111998--c65e9e57fad097d581c969964001670f.nii.gz \ No newline at end of file diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index d4941e6dd..000000000 --- a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:07:15.775000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99943, - -0.0337242, - 0.00171381, - 0.0319322, - 0.92738, - -0.372756 - ], - "ImageOrientationText": 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"TotalReadoutTime": 0.0576811, - "TxRefAmp": 286.202, - "WipMemBlock": "7fa6d61b-40f8-4584-b83f-80c5163be30a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 9f5a3c81c..000000000 --- a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/2p/mk/MD5E-s1103541--a932f344a7fafd946e9dc115728939d4.nii.gz/MD5E-s1103541--a932f344a7fafd946e9dc115728939d4.nii.gz \ No newline at end of file diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 7c1585e32..000000000 --- a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:15:59.907500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99943, - -0.0337242, - 0.00171381, - 0.0319322, - 0.92738, - -0.372756 - ], - "ImageOrientationText": "Tra>Cor(-21.9)>Sag(-0.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0726219, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 589, - -7297, - -8821, - 389, - 47, - -370, - -32, - 109 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 286.202, - "WipMemBlock": "093e2dd8-add7-4244-8f1f-bafc09f556fc||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 29e1751bc..000000000 --- a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/gg/gW/MD5E-s1103596--f0d918c9d8d11cd8097c04332495ca5a.nii.gz/MD5E-s1103596--f0d918c9d8d11cd8097c04332495ca5a.nii.gz \ No newline at end of file diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 2f0d927e7..000000000 --- a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:33:40.220000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99943, - -0.0337242, - 0.00171381, - 0.0319322, - 0.92738, - -0.372756 - ], - "ImageOrientationText": "Tra>Cor(-21.9)>Sag(-0.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0726219, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 589, - -7297, - -8821, - 389, - 47, - -370, - -32, - 109 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 286.202, - "WipMemBlock": "b95d6276-67b3-4e6a-9d58-bb6c0f8ebda4||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 5fe635e45..000000000 --- a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/pZ/ZW/MD5E-s1103743--b2803d1a9683b99aa7c39aef2e7a80f2.nii.gz/MD5E-s1103743--b2803d1a9683b99aa7c39aef2e7a80f2.nii.gz \ No newline at end of file diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 3e4fea479..000000000 --- a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:42:18.650000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99943, - -0.0337242, - 0.00171381, - 0.0319322, - 0.92738, - -0.372756 - ], - "ImageOrientationText": "Tra>Cor(-21.9)>Sag(-0.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0726219, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 589, - -7297, - -8821, - 389, - 47, - -370, - -32, - 109 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 286.202, - "WipMemBlock": "cc853b59-d3a2-4f09-8043-cc1bff975e2f||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 59db7c996..000000000 --- a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Pv/JV/MD5E-s1103373--2b65875037f3b173bf35971ffa3b0c73.nii.gz/MD5E-s1103373--2b65875037f3b173bf35971ffa3b0c73.nii.gz \ No newline at end of file diff --git a/sub-05/ses-005/sub-05_ses-005_scans.tsv b/sub-05/ses-005/sub-05_ses-005_scans.tsv index 70631ff19..b1fbfafb9 120000 --- a/sub-05/ses-005/sub-05_ses-005_scans.tsv +++ b/sub-05/ses-005/sub-05_ses-005_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/22/QG/MD5E-s3289--c49d00327ed30a28fd61cd5703c7f50f.tsv/MD5E-s3289--c49d00327ed30a28fd61cd5703c7f50f.tsv \ No newline at end of file +../../.git/annex/objects/8z/vg/MD5E-s2567--a7c11050d1d493f316bb475c2724b1ef.tsv/MD5E-s2567--a7c11050d1d493f316bb475c2724b1ef.tsv \ No newline at end of file From 62d03a6ca9e7f48898f8bc1ae33e7fcda70bdb52 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:28:16 -0400 Subject: [PATCH 224/463] fix complex event files --- ...g_events.tsv => sub-05_ses-005_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-05_ses-005_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-05_ses-005_task-mario3_run-03_events.tsv} | 0 .../func/sub-05_ses-005_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-05_ses-005_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-05_ses-005_task-mario3_run-04_events.tsv} | 0 .../func/sub-05_ses-005_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-05_ses-005_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-05/ses-005/func/{sub-05_ses-005_task-mario3_run-01_part-mag_events.tsv => sub-05_ses-005_task-mario3_run-01_events.tsv} (100%) rename sub-05/ses-005/func/{sub-05_ses-005_task-mario3_run-01_part-phase_events.tsv => sub-05_ses-005_task-mario3_run-02_events.tsv} (100%) rename sub-05/ses-005/func/{sub-05_ses-005_task-mario3_run-02_part-mag_events.tsv => sub-05_ses-005_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-03_part-phase_events.tsv rename sub-05/ses-005/func/{sub-05_ses-005_task-mario3_run-02_part-phase_events.tsv => sub-05_ses-005_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-01_part-mag_events.tsv b/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-01_events.tsv similarity index 100% rename from sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-01_part-mag_events.tsv rename to sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-01_events.tsv diff --git a/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-01_part-phase_events.tsv b/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-02_events.tsv similarity index 100% rename from sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-01_part-phase_events.tsv rename to sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-02_events.tsv diff --git a/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-02_part-mag_events.tsv b/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-03_events.tsv similarity index 100% rename from sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-02_part-mag_events.tsv rename to sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-03_events.tsv diff --git a/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-03_part-mag_events.tsv b/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-03_part-phase_events.tsv b/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-02_part-phase_events.tsv b/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_events.tsv similarity index 100% rename from sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-02_part-phase_events.tsv rename to sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_events.tsv diff --git a/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_part-mag_events.tsv b/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_part-phase_events.tsv b/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-005/func/sub-05_ses-005_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From d086a564d2ee1ed054cba9449560617664c99734 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:29:23 -0400 Subject: [PATCH 225/463] fill IntendedFor --- ...5_ses-005_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...5_ses-005_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...5_ses-005_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...5_ses-005_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...5_ses-005_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_epi.json b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_epi.json index abfaaab47..eff1fd99e 100644 --- a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99943, - -0.0337242, - 0.00171381, - 0.0319322, - 0.92738, - -0.372756 - ], + "ImageOrientationPatientDICOM": [0.99943, -0.0337242, 0.00171381, 0.0319322, 0.92738, -0.372756], "ImageOrientationText": "Tra>Cor(-21.9)>Sag(-0.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-05_ses-005_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-005/func/sub-05_ses-005_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-005/func/sub-05_ses-005_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-005/func/sub-05_ses-005_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 589, - -7297, - -8821, - 389, - 47, - -370, - -32, - 109 - ], + "ShimSetting": [589, -7297, -8821, 389, 47, -370, -32, 109], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_epi.json b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_epi.json index 889871060..b014c8306 100644 --- a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99943, - -0.0337242, - 0.00171381, - 0.0319322, - 0.92738, - -0.372756 - ], + "ImageOrientationPatientDICOM": [0.99943, -0.0337242, 0.00171381, 0.0319322, 0.92738, -0.372756], "ImageOrientationText": "Tra>Cor(-21.9)>Sag(-0.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-05_ses-005_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 589, - -7297, - -8821, - 389, - 47, - -370, - -32, - 109 - ], + "ShimSetting": [589, -7297, -8821, 389, 47, -370, -32, 109], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_epi.json b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_epi.json index b9e547918..c6955f127 100644 --- a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99943, - -0.0337242, - 0.00171381, - 0.0319322, - 0.92738, - -0.372756 - ], + "ImageOrientationPatientDICOM": [0.99943, -0.0337242, 0.00171381, 0.0319322, 0.92738, -0.372756], "ImageOrientationText": "Tra>Cor(-21.9)>Sag(-0.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-05_ses-005_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 589, - -7297, - -8821, - 389, - 47, - -370, - -32, - 109 - ], + "ShimSetting": [589, -7297, -8821, 389, 47, -370, -32, 109], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_epi.json b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_epi.json index 4d0ffe607..4d5a1d50f 100644 --- a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99943, - -0.0337242, - 0.00171381, - 0.0319322, - 0.92738, - -0.372756 - ], + "ImageOrientationPatientDICOM": [0.99943, -0.0337242, 0.00171381, 0.0319322, 0.92738, -0.372756], "ImageOrientationText": "Tra>Cor(-21.9)>Sag(-0.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-05_ses-005_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 589, - -7297, - -8821, - 389, - 47, - -370, - -32, - 109 - ], + "ShimSetting": [589, -7297, -8821, 389, 47, -370, -32, 109], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_epi.json b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_epi.json index 15aa577c9..09ec7317c 100644 --- a/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-05/ses-005/fmap/sub-05_ses-005_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99943, - -0.0337242, - 0.00171381, - 0.0319322, - 0.92738, - -0.372756 - ], + "ImageOrientationPatientDICOM": [0.99943, -0.0337242, 0.00171381, 0.0319322, 0.92738, -0.372756], "ImageOrientationText": "Tra>Cor(-21.9)>Sag(-0.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-05_ses-005_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 589, - -7297, - -8821, - 389, - 47, - -370, - -32, - 109 - ], + "ShimSetting": [589, -7297, -8821, 389, 47, -370, -32, 109], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 01555231ade1a4002339e0823f22f3864b539c5e Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:31:38 -0400 Subject: [PATCH 226/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..9b8cc7604 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 5f1d300e-223e-4894-ad92-8f6ed92e3b28 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..63418481f --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 63418481f33c0d61fc1ab0769871de1c4cfd5807 From 1e7e37bfe5cf0b78110a3e271bef08515199f416 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:33:36 -0400 Subject: [PATCH 227/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-03_ses-011_acq-axial_localizer.json | 81 +++ .../sub-03_ses-011_acq-axial_localizer.nii.gz | 1 + .../sub-03_ses-011_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-011_acq-coronal_localizer.nii.gz | 1 + ...sub-03_ses-011_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-011_acq-sagittal_localizer.nii.gz | 1 + sub-03/ses-011/anat/sub-03_ses-011_scout.json | 542 ++++++++++++++++++ .../ses-011/anat/sub-03_ses-011_scout.nii.gz | 1 + ...1_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-011_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...11_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...011_task-mario3_run-01_part-mag_events.tsv | 1 + ...011_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...11_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-01_part-phase_events.tsv | 1 + ...1_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-011_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...11_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...011_task-mario3_run-02_part-mag_events.tsv | 1 + ...011_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...11_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-02_part-phase_events.tsv | 1 + ...1_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-011_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...11_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...011_task-mario3_run-03_part-mag_events.tsv | 1 + ...011_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...11_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-03_part-phase_events.tsv | 1 + ...1_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-011_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...11_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...011_task-mario3_run-04_part-mag_events.tsv | 1 + ...011_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...11_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-04_part-phase_events.tsv | 1 + ...1_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-03/ses-011/sub-03_ses-011_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5409 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-011/anat/sub-03_ses-011_acq-axial_localizer.json create mode 120000 sub-03/ses-011/anat/sub-03_ses-011_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-011/anat/sub-03_ses-011_acq-coronal_localizer.json create mode 120000 sub-03/ses-011/anat/sub-03_ses-011_acq-coronal_localizer.nii.gz create mode 100644 sub-03/ses-011/anat/sub-03_ses-011_acq-sagittal_localizer.json create mode 120000 sub-03/ses-011/anat/sub-03_ses-011_acq-sagittal_localizer.nii.gz create mode 100644 sub-03/ses-011/anat/sub-03_ses-011_scout.json create mode 120000 sub-03/ses-011/anat/sub-03_ses-011_scout.nii.gz create mode 100644 sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_part-phase_sbref.nii.gz create mode 120000 sub-03/ses-011/sub-03_ses-011_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index b2f5f6097..737e9e4d6 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit b2f5f6097e6be93eaeb37ca48a0806a853f0c927 +Subproject commit 737e9e4d609a892fb4f457b6ed10ae3c461df486 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-03/ses-011/anat/sub-03_ses-011_acq-axial_localizer.json b/sub-03/ses-011/anat/sub-03_ses-011_acq-axial_localizer.json new file mode 100644 index 000000000..4bdda188a --- /dev/null +++ b/sub-03/ses-011/anat/sub-03_ses-011_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + 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a/sub-03/ses-011/sub-03_ses-011_scans.tsv b/sub-03/ses-011/sub-03_ses-011_scans.tsv new file mode 120000 index 000000000..9a8da747a --- /dev/null +++ b/sub-03/ses-011/sub-03_ses-011_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/ZW/x5/MD5E-s3289--d0b0c890882b5c66fe292af977a1c027.tsv/MD5E-s3289--d0b0c890882b5c66fe292af977a1c027.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..c3954cd71 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": 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"PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.057658, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [614, -7243, -8765, 678, 62, -34, 89, -7], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 239.583, + "dcmmeta_affine": [ + [-1.9996180534362793, -0.03211071714758873, 0.022285541519522667, 110.02725982666016], + [-0.03642333671450615, 1.9445334672927856, -0.46632909774780273, -73.75045013427734], + [0.014180409722030163, 0.46664589643478394, 1.9447468519210815, -49.40635299682617], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From acae8629c9b3deaf9d0905c22da23d8cae4b109e Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:34:22 -0400 Subject: [PATCH 228/463] fix fmap phase --- ...3_ses-011_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-011_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-011_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-011_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-011_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-011_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-011_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-03/ses-011/sub-03_ses-011_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-03/ses-011/fmap/{sub-03_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-011_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-011/fmap/{sub-03_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-011_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-011/fmap/{sub-03_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-011_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-011/fmap/{sub-03_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-011_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-011/fmap/{sub-03_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-011_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-011/fmap/{sub-03_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-011_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-011/fmap/{sub-03_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-011_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-011/fmap/{sub-03_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-011_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-03/ses-011/fmap/{sub-03_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-03_ses-011_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-03/ses-011/fmap/{sub-03_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-03_ses-011_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-03/ses-011/fmap/{sub-03_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-03_ses-011_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-03/ses-011/fmap/{sub-03_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-03_ses-011_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 7394567ef..000000000 --- a/sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "17:53:51.402500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999809, 0.0182117, 0.0070902, -0.0160554, 0.972267, -0.233323], - "ImageOrientationText": "Tra>Cor(-13.5)>Sag(0.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0459825, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [614, -7243, -8765, 678, 62, -34, 89, -7], - "SliceThickness": 2, - "SliceTiming": [0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 239.583, - "WipMemBlock": "308d790c-61b1-4962-b4ea-b7c7fa08ee06||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9996180534362793, -0.03211071714758873, 0.022285541519522667, 110.02725982666016], - [-0.03642333671450615, 1.9445334672927856, -0.46632909774780273, -73.75045013427734], - [0.014180409722030163, 0.46664589643478394, 1.9447468519210815, -49.40635299682617], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.9998090138162, 0.0182116689378, 0.00709020496008, -0.0160553589917, 0.97226674801592, -0.2333229439001], - "ImagePositionPatient": [-822.89251614052, -847.60478965537, 163.35560553391], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.260242, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "175141.053000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.04598250487658, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "175436.725000", - "SliceLocation": -29.619429598428, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999831585, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "175140.983000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["175351.402500", "175352.892500", "175354.382500"], - "ContentTime": ["175436.727000", "175437.922000", "175437.925000"], - "InstanceCreationTime": ["175436.727000", "175437.922000", "175437.925000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4864.0, 4862.0, 4866.0], - "WindowWidth": [18602.0, 18608.0, 18606.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 3667c038c..000000000 --- a/sub-03/ses-011/fmap/sub-03_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/kf/ZX/MD5E-s3334110--988964351ace943f165849b76f481694.nii.gz/MD5E-s3334110--988964351ace943f165849b76f481694.nii.gz \ No newline at end of file diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 02296354f..000000000 --- a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "17:53:40.972500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999809, - 0.0182117, - 0.0070902, - -0.0160554, - 0.972267, - -0.233323 - ], - "ImageOrientationText": "Tra>Cor(-13.5)>Sag(0.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0459825, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 614, - -7243, - -8765, - 678, - 62, - -34, - 89, - -7 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 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-../../../.git/annex/objects/PF/68/MD5E-s1112119--a9d94a4eda357515fdfc3fdb0d67a573.nii.gz/MD5E-s1112119--a9d94a4eda357515fdfc3fdb0d67a573.nii.gz \ No newline at end of file diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 0f10592dd..000000000 --- a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "17:54:56.325000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index c3fce0e87..000000000 --- a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:13:27.047500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of 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b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 160b41893..000000000 --- a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/5z/9F/MD5E-s1103618--7d55b5e0504b38ff591d64f0aaa8678c.nii.gz/MD5E-s1103618--7d55b5e0504b38ff591d64f0aaa8678c.nii.gz \ No newline at end of file diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index c05392692..000000000 --- a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:24:58.840000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999809, - 0.0182117, - 0.0070902, - -0.0160554, - 0.972267, - -0.233323 - ], - "ImageOrientationText": "Tra>Cor(-13.5)>Sag(0.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.057658, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 614, - -7243, - -8765, - 678, - 62, - -34, - 89, - -7 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 239.583, - "WipMemBlock": "486de44d-8a11-4f9e-a61d-909897eac2ea||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 267733838..000000000 --- a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/kP/7V/MD5E-s1103616--efa790c9366fecbcd783b16c5e81e100.nii.gz/MD5E-s1103616--efa790c9366fecbcd783b16c5e81e100.nii.gz \ No newline at end of file diff --git a/sub-03/ses-011/sub-03_ses-011_scans.tsv b/sub-03/ses-011/sub-03_ses-011_scans.tsv index 9a8da747a..c779312a9 120000 --- a/sub-03/ses-011/sub-03_ses-011_scans.tsv +++ b/sub-03/ses-011/sub-03_ses-011_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/ZW/x5/MD5E-s3289--d0b0c890882b5c66fe292af977a1c027.tsv/MD5E-s3289--d0b0c890882b5c66fe292af977a1c027.tsv \ No newline at end of file +../../.git/annex/objects/Zf/28/MD5E-s2567--ac2d824dd0ae9895ff1826f6e64372c5.tsv/MD5E-s2567--ac2d824dd0ae9895ff1826f6e64372c5.tsv \ No newline at end of file From c48318d1b1e7adb5b596349e0cb3196971690979 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:34:32 -0400 Subject: [PATCH 229/463] fix complex event files --- ...g_events.tsv => sub-03_ses-011_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-03_ses-011_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-03_ses-011_task-mario3_run-03_events.tsv} | 0 .../func/sub-03_ses-011_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-03_ses-011_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-03_ses-011_task-mario3_run-04_events.tsv} | 0 .../func/sub-03_ses-011_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-03_ses-011_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-03/ses-011/func/{sub-03_ses-011_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-011_task-mario3_run-01_events.tsv} (100%) rename sub-03/ses-011/func/{sub-03_ses-011_task-mario3_run-01_part-phase_events.tsv => sub-03_ses-011_task-mario3_run-02_events.tsv} (100%) rename sub-03/ses-011/func/{sub-03_ses-011_task-mario3_run-02_part-mag_events.tsv => sub-03_ses-011_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_part-phase_events.tsv rename sub-03/ses-011/func/{sub-03_ses-011_task-mario3_run-02_part-phase_events.tsv => sub-03_ses-011_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-02_events.tsv similarity index 100% rename from sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-01_part-phase_events.tsv rename to sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-02_events.tsv diff --git a/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-02_part-mag_events.tsv b/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_events.tsv similarity index 100% rename from sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-02_part-mag_events.tsv rename to sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_events.tsv diff --git a/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_part-mag_events.tsv b/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_part-phase_events.tsv b/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-02_part-phase_events.tsv b/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_events.tsv similarity index 100% rename from sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-02_part-phase_events.tsv rename to sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_events.tsv diff --git a/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_part-mag_events.tsv b/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_part-phase_events.tsv b/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-011/func/sub-03_ses-011_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 993d381a82b1ef1468e766b4e1234f42ffb8210b Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:36:11 -0400 Subject: [PATCH 230/463] fill IntendedFor --- ...3_ses-011_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...3_ses-011_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...3_ses-011_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...3_ses-011_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...3_ses-011_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_epi.json index 520e66451..4b0958f94 100644 --- a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999809, - 0.0182117, - 0.0070902, - -0.0160554, - 0.972267, - -0.233323 - ], + "ImageOrientationPatientDICOM": [0.999809, 0.0182117, 0.0070902, -0.0160554, 0.972267, -0.233323], "ImageOrientationText": "Tra>Cor(-13.5)>Sag(0.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-03_ses-011_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-011/func/sub-03_ses-011_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-011/func/sub-03_ses-011_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-011/func/sub-03_ses-011_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 614, - -7243, - -8765, - 678, - 62, - -34, - 89, - -7 - ], + "ShimSetting": [614, -7243, -8765, 678, 62, -34, 89, -7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_epi.json b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_epi.json index e751d19a8..7d2c34da3 100644 --- a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999809, - 0.0182117, - 0.0070902, - -0.0160554, - 0.972267, - -0.233323 - ], + "ImageOrientationPatientDICOM": [0.999809, 0.0182117, 0.0070902, -0.0160554, 0.972267, -0.233323], "ImageOrientationText": "Tra>Cor(-13.5)>Sag(0.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-03_ses-011_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 614, - -7243, - -8765, - 678, - 62, - -34, - 89, - -7 - ], + "ShimSetting": [614, -7243, -8765, 678, 62, -34, 89, -7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-02_epi.json b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-02_epi.json index 7e2f71f18..37640b7a9 100644 --- a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999809, - 0.0182117, - 0.0070902, - -0.0160554, - 0.972267, - -0.233323 - ], + "ImageOrientationPatientDICOM": [0.999809, 0.0182117, 0.0070902, -0.0160554, 0.972267, -0.233323], "ImageOrientationText": "Tra>Cor(-13.5)>Sag(0.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-03_ses-011_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 614, - -7243, - -8765, - 678, - 62, - -34, - 89, - -7 - ], + "ShimSetting": [614, -7243, -8765, 678, 62, -34, 89, -7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_epi.json b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_epi.json index 28e53f18e..c0913c4ba 100644 --- a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999809, - 0.0182117, - 0.0070902, - -0.0160554, - 0.972267, - -0.233323 - ], + "ImageOrientationPatientDICOM": [0.999809, 0.0182117, 0.0070902, -0.0160554, 0.972267, -0.233323], "ImageOrientationText": "Tra>Cor(-13.5)>Sag(0.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-03_ses-011_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 614, - -7243, - -8765, - 678, - 62, - -34, - 89, - -7 - ], + "ShimSetting": [614, -7243, -8765, 678, 62, -34, 89, -7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_epi.json b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_epi.json index 489083b42..31ff02eb4 100644 --- a/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-03/ses-011/fmap/sub-03_ses-011_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999809, - 0.0182117, - 0.0070902, - -0.0160554, - 0.972267, - -0.233323 - ], + "ImageOrientationPatientDICOM": [0.999809, 0.0182117, 0.0070902, -0.0160554, 0.972267, -0.233323], "ImageOrientationText": "Tra>Cor(-13.5)>Sag(0.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-03_ses-011_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 614, - -7243, - -8765, - 678, - 62, - -34, - 89, - -7 - ], + "ShimSetting": [614, -7243, -8765, 678, 62, -34, 89, -7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From d21a12c74601b49fd7e515fd6cc7139fcc32724f Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:36:58 -0400 Subject: [PATCH 231/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-017_acq-axial_localizer.json | 81 +++ .../sub-01_ses-017_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-017_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-017_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-017_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-017_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-017/anat/sub-01_ses-017_scout.json | 542 ++++++++++++++++++ .../ses-017/anat/sub-01_ses-017_scout.nii.gz | 1 + ...7_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ...-017_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...017_task-mario3_run-01_part-mag_events.tsv | 1 + ...017_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-01_part-phase_events.tsv | 1 + ...7_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-017_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...017_task-mario3_run-02_part-mag_events.tsv | 1 + ...017_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-02_part-phase_events.tsv | 1 + ...7_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-017_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...017_task-mario3_run-03_part-mag_events.tsv | 1 + ...017_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-03_part-phase_events.tsv | 1 + ...7_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-017_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...017_task-mario3_run-04_part-mag_events.tsv | 1 + ...017_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-04_part-phase_events.tsv | 1 + ...7_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-017_task-mario3_run-05_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...017_task-mario3_run-05_part-mag_events.tsv | 1 + ...017_task-mario3_run-05_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-05_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-05_part-phase_events.tsv | 1 + ...7_task-mario3_run-05_part-phase_sbref.json | 153 +++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + sub-01/ses-017/sub-01_ses-017_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 93 files changed, 6371 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-017/anat/sub-01_ses-017_acq-axial_localizer.json create mode 120000 sub-01/ses-017/anat/sub-01_ses-017_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-017/anat/sub-01_ses-017_acq-coronal_localizer.json create mode 120000 sub-01/ses-017/anat/sub-01_ses-017_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-017/anat/sub-01_ses-017_acq-sagittal_localizer.json create mode 120000 sub-01/ses-017/anat/sub-01_ses-017_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-017/anat/sub-01_ses-017_scout.json create mode 120000 sub-01/ses-017/anat/sub-01_ses-017_scout.nii.gz create mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 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fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-017/anat/sub-01_ses-017_acq-axial_localizer.json b/sub-01/ses-017/anat/sub-01_ses-017_acq-axial_localizer.json new file mode 100644 index 000000000..d4d06e6c3 --- /dev/null +++ b/sub-01/ses-017/anat/sub-01_ses-017_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:19:30.020000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0454157, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 291.322 +} \ No newline at end of file diff --git a/sub-01/ses-017/anat/sub-01_ses-017_acq-axial_localizer.nii.gz b/sub-01/ses-017/anat/sub-01_ses-017_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..37168a653 --- /dev/null +++ b/sub-01/ses-017/anat/sub-01_ses-017_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/GM/VM/MD5E-s181276--c9f1cbcb0b43d3e3603046c0de1da8fc.nii.gz/MD5E-s181276--c9f1cbcb0b43d3e3603046c0de1da8fc.nii.gz \ No newline at end of file diff --git a/sub-01/ses-017/anat/sub-01_ses-017_acq-coronal_localizer.json b/sub-01/ses-017/anat/sub-01_ses-017_acq-coronal_localizer.json new file mode 100644 index 000000000..ae395e64b --- /dev/null +++ b/sub-01/ses-017/anat/sub-01_ses-017_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:19:37.010000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0454157, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 291.322 +} \ No newline at end of file diff --git a/sub-01/ses-017/anat/sub-01_ses-017_acq-coronal_localizer.nii.gz b/sub-01/ses-017/anat/sub-01_ses-017_acq-coronal_localizer.nii.gz new file mode 120000 index 000000000..d45459b05 --- /dev/null +++ b/sub-01/ses-017/anat/sub-01_ses-017_acq-coronal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/KP/GK/MD5E-s199720--25362f8cbc518467520ffd3663f28f7e.nii.gz/MD5E-s199720--25362f8cbc518467520ffd3663f28f7e.nii.gz \ No newline at end of file diff --git a/sub-01/ses-017/anat/sub-01_ses-017_acq-sagittal_localizer.json b/sub-01/ses-017/anat/sub-01_ses-017_acq-sagittal_localizer.json new file mode 100644 index 000000000..75a27582c --- /dev/null +++ b/sub-01/ses-017/anat/sub-01_ses-017_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:19:23.030000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 0, + 1, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Sag", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0454157, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SliceTiming": [ + 0, + 10.4844, + 3.49219 + ], + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 28, + "StationName": "MRC35049", + "TxRefAmp": 291.322 +} \ No newline at end of file diff --git a/sub-01/ses-017/anat/sub-01_ses-017_acq-sagittal_localizer.nii.gz b/sub-01/ses-017/anat/sub-01_ses-017_acq-sagittal_localizer.nii.gz new file mode 120000 index 000000000..279bc3e6c --- /dev/null +++ b/sub-01/ses-017/anat/sub-01_ses-017_acq-sagittal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/V1/Gp/MD5E-s637781--e9437153674d90acdd8141adad031b0f.nii.gz/MD5E-s637781--e9437153674d90acdd8141adad031b0f.nii.gz \ No newline at end of file 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"SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 291.322, + "dcmmeta_affine": [ + [-1.9890543222427368, -0.1722707599401474, 0.1182602196931839, 110.77277374267578], + [-0.200455442070961, 1.8927042484283447, -0.6144006252288818, -52.15912628173828], + [0.05899418517947197, 0.6228910684585571, 1.8996121883392334, -52.513362884521484], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 27926c98da540c090de75e7e5ad6ea257597f3ac Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:37:42 -0400 Subject: [PATCH 232/463] fix fmap phase --- ...1_ses-017_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-017_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-017_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - sub-01/ses-017/sub-01_ses-017_scans.tsv | 2 +- 29 files changed, 1 insertion(+), 1097 deletions(-) rename sub-01/ses-017/fmap/{sub-01_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-017_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-017/fmap/{sub-01_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-017_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-017/fmap/{sub-01_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-017_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-017/fmap/{sub-01_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-017_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-017/fmap/{sub-01_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-017_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-017/fmap/{sub-01_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-017_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-017/fmap/{sub-01_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-017_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-017/fmap/{sub-01_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-017_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-01/ses-017/fmap/{sub-01_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-01_ses-017_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-01/ses-017/fmap/{sub-01_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-01_ses-017_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-01/ses-017/fmap/{sub-01_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-01_ses-017_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-01/ses-017/fmap/{sub-01_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-01_ses-017_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-01/ses-017/fmap/{sub-01_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-01_ses-017_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-01/ses-017/fmap/{sub-01_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-01_ses-017_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 1af5803da..000000000 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:20:29.420000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.994527, 0.100228, 0.0294971, -0.0861354, 0.946352, -0.311446], - "ImageOrientationText": 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"HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0533473, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [622, -7195, -8782, 671, 107, 20, -26, 20], - "SliceThickness": 2, - "SliceTiming": [0, 0.7825, 0.0975, 0.88, 0.195, 0.98, 0.2925, 1.0775, 0.39, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685, 0, 0.7825, 0.0975, 0.88, 0.195, 0.98, 0.2925, 1.0775, 0.39, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685, 0, 0.7825, 0.0975, 0.88, 0.195, 0.98, 0.2925, 1.0775, 0.39, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685, 0, 0.7825, 0.0975, 0.88, 0.195, 0.98, 0.2925, 1.0775, 0.39, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 291.322, - "WipMemBlock": "3b1c7a9d-3827-4a11-87a1-0cd901317482||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9890543222427368, -0.1722707599401474, 0.1182602196931839, 110.77277374267578], - [-0.200455442070961, 1.8927042484283447, -0.6144006252288818, -52.15912628173828], - [0.05899418517947197, 0.6228910684585571, 1.8996121883392334, -52.513362884521484], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99452718727261, 0.10022771750882, 0.02949709169753, -0.0861353799, 0.94635213869673, 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"ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "112115.123000", - "SliceLocation": -27.304205771601, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.999999961631, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "2", - "StudyTime": "111840.440000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["112029.420000", "112030.910000", "112032.400000"], - "ContentTime": ["112115.125000", "112115.128000", "112115.131000"], - "InstanceCreationTime": ["112115.125000", "112115.128000", "112115.131000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4792.0, 4788.0, 4790.0], - "WindowWidth": [18572.0, 18572.0, 18570.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 4b6d715d3..000000000 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/6q/G1/MD5E-s3335209--4dd4c6c5390e1d5e262b3a019dfd2126.nii.gz/MD5E-s3335209--4dd4c6c5390e1d5e262b3a019dfd2126.nii.gz \ No newline at end of file diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 4baf7f38b..000000000 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:20:18.990000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994527, - 0.100228, - 0.0294971, - -0.0861354, - 0.946352, - -0.311446 - ], - "ImageOrientationText": "Tra>Cor(-17.9)>Sag(3.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0533473, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 622, - -7195, - -8782, - 671, - 107, - 20, - -26, - 20 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 291.322, - "WipMemBlock": "3b1c7a9d-3827-4a11-87a1-0cd901317482||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 29beb9c59..000000000 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Z2/q2/MD5E-s1112389--5f8e93b21fc66c519b15fb6304cfad7b.nii.gz/MD5E-s1112389--5f8e93b21fc66c519b15fb6304cfad7b.nii.gz \ No newline at end of file diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 6af45e972..000000000 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:21:34.805000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994527, - 0.100228, - 0.0294971, - -0.0861354, - 0.946352, - -0.311446 - ], - "ImageOrientationText": "Tra>Cor(-17.9)>Sag(3.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0668929, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 622, - -7195, - -8782, - 671, - 107, - 20, - -26, - 20 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 291.322, - "WipMemBlock": "92056720-b167-4e87-a654-b74ece94c4b9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 23097a28a..000000000 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/QK/JK/MD5E-s1104006--5a36ed779d5564e9c5df7d4da569401e.nii.gz/MD5E-s1104006--5a36ed779d5564e9c5df7d4da569401e.nii.gz \ No newline at end of file diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 22ba8e2cc..000000000 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:31:8.227500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994527, - 0.100228, - 0.0294971, - -0.0861354, - 0.946352, - -0.311446 - ], - "ImageOrientationText": "Tra>Cor(-17.9)>Sag(3.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0668929, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 622, - -7195, - -8782, - 671, - 107, - 20, - -26, - 20 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 291.322, - "WipMemBlock": "5461a2a1-729c-468d-844a-695c776fb61e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 05235b7c6..000000000 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Xq/X5/MD5E-s1103866--332687347ae0a8f164d55d2eec250203.nii.gz/MD5E-s1103866--332687347ae0a8f164d55d2eec250203.nii.gz \ No newline at end of file diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index a2ea59fc3..000000000 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:48:19.952500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994527, - 0.100228, - 0.0294971, - -0.0861354, - 0.946352, - -0.311446 - ], - "ImageOrientationText": "Tra>Cor(-17.9)>Sag(3.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0668929, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 622, - -7195, - -8782, - 671, - 107, - 20, - -26, - 20 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 291.322, - "WipMemBlock": "da9364eb-8bfc-4f5d-9e16-a5daa9259400||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 8822b038b..000000000 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/k6/Q5/MD5E-s1103784--7e659d8e1f01dc854aa69f36b0ab309b.nii.gz/MD5E-s1103784--7e659d8e1f01dc854aa69f36b0ab309b.nii.gz \ No newline at end of file diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index c18c1aa86..000000000 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:58:47.710000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994527, - 0.100228, - 0.0294971, - -0.0861354, - 0.946352, - -0.311446 - ], - "ImageOrientationText": "Tra>Cor(-17.9)>Sag(3.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0668929, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 622, - -7195, - -8782, - 671, - 107, - 20, - -26, - 20 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 291.322, - "WipMemBlock": "bc152ec8-eaee-4623-a030-4f07c43eed9a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index bc7acff4b..000000000 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Gz/0w/MD5E-s1103772--773d778baf9b415ad89bd687cd9c5a44.nii.gz/MD5E-s1103772--773d778baf9b415ad89bd687cd9c5a44.nii.gz \ No newline at end of file diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index 7a382dfc6..000000000 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "12:10:34.402500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994527, - 0.100228, - 0.0294971, - -0.0861354, - 0.946352, - -0.311446 - ], - "ImageOrientationText": "Tra>Cor(-17.9)>Sag(3.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-05", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0668929, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 622, - -7195, - -8782, - 671, - 107, - 20, - -26, - 20 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 291.322, - "WipMemBlock": "aad0d614-1c70-4202-ab22-48b604550c51||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index 3f3112593..000000000 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Kx/w8/MD5E-s1103899--7ecfaf5e0c7f6691eb4e537c540ea9a5.nii.gz/MD5E-s1103899--7ecfaf5e0c7f6691eb4e537c540ea9a5.nii.gz \ No newline at end of file diff --git a/sub-01/ses-017/sub-01_ses-017_scans.tsv b/sub-01/ses-017/sub-01_ses-017_scans.tsv index c00ec37ba..ebb40e02f 120000 --- a/sub-01/ses-017/sub-01_ses-017_scans.tsv +++ b/sub-01/ses-017/sub-01_ses-017_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/Pm/p8/MD5E-s3904--24518710c6b9702d6a4a157ad2176202.tsv/MD5E-s3904--24518710c6b9702d6a4a157ad2176202.tsv \ No newline at end of file +../../.git/annex/objects/8M/13/MD5E-s3061--ac56f7dd3b1196c95ae346cbdc725258.tsv/MD5E-s3061--ac56f7dd3b1196c95ae346cbdc725258.tsv \ No newline at end of file From e67ca82a7dc706764afcf263068e0c5fe4bf2738 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:37:51 -0400 Subject: [PATCH 233/463] fix complex event files --- ...g_events.tsv => sub-01_ses-017_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-017_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-01_ses-017_task-mario3_run-03_events.tsv} | 0 .../func/sub-01_ses-017_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-01_ses-017_task-mario3_run-04_events.tsv} | 0 .../func/sub-01_ses-017_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-01_ses-017_task-mario3_run-04_part-phase_events.tsv | 1 - ...g_events.tsv => sub-01_ses-017_task-mario3_run-05_events.tsv} | 0 .../func/sub-01_ses-017_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-01_ses-017_task-mario3_run-05_part-phase_events.tsv | 1 - 10 files changed, 5 deletions(-) rename sub-01/ses-017/func/{sub-01_ses-017_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-017_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-017/func/{sub-01_ses-017_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-017_task-mario3_run-02_events.tsv} (100%) rename sub-01/ses-017/func/{sub-01_ses-017_task-mario3_run-02_part-mag_events.tsv => sub-01_ses-017_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-03_part-phase_events.tsv rename sub-01/ses-017/func/{sub-01_ses-017_task-mario3_run-02_part-phase_events.tsv => sub-01_ses-017_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-04_part-phase_events.tsv rename sub-01/ses-017/func/{sub-01_ses-017_task-mario3_run-03_part-mag_events.tsv => sub-01_ses-017_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-05_part-phase_events.tsv diff --git a/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-03_events.tsv similarity index 100% rename from sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-02_part-mag_events.tsv rename to sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-03_events.tsv diff --git a/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-04_events.tsv similarity index 100% rename from sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-02_part-phase_events.tsv rename to sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-04_events.tsv diff --git a/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-04_part-mag_events.tsv b/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-04_part-phase_events.tsv b/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-03_part-mag_events.tsv b/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-05_events.tsv similarity index 100% rename from sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-03_part-mag_events.tsv rename to sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-05_events.tsv diff --git a/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-05_part-mag_events.tsv b/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-05_part-phase_events.tsv b/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-017/func/sub-01_ses-017_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From b2517c06054b9dcfa8ccbd0e935c839b7f0b7146 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:38:49 -0400 Subject: [PATCH 234/463] fill IntendedFor --- ...1_ses-017_acq-sbref_dir-AP_run-01_epi.json | 92 +++---------------- ...1_ses-017_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...1_ses-017_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...1_ses-017_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...1_ses-017_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- ...1_ses-017_acq-sbref_dir-PA_run-05_epi.json | 88 ++---------------- 6 files changed, 46 insertions(+), 486 deletions(-) diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_epi.json index f93748d88..41a17c260 100644 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994527, - 0.100228, - 0.0294971, - -0.0861354, - 0.946352, - -0.311446 - ], + "ImageOrientationPatientDICOM": [0.994527, 0.100228, 0.0294971, -0.0861354, 0.946352, -0.311446], "ImageOrientationText": "Tra>Cor(-17.9)>Sag(3.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,19 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-01_ses-017_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-017/func/sub-01_ses-017_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-017/func/sub-01_ses-017_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-017/func/sub-01_ses-017_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-017/func/sub-01_ses-017_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +67,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 622, - -7195, - -8782, - 671, - 107, - 20, - -26, - 20 - ], + "ShimSetting": [622, -7195, -8782, 671, 107, 20, -26, 20], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_epi.json index 7ac617669..fe4980d95 100644 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994527, - 0.100228, - 0.0294971, - -0.0861354, - 0.946352, - -0.311446 - ], + "ImageOrientationPatientDICOM": [0.994527, 0.100228, 0.0294971, -0.0861354, 0.946352, -0.311446], "ImageOrientationText": "Tra>Cor(-17.9)>Sag(3.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-01_ses-017_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 622, - -7195, - -8782, - 671, - 107, - 20, - -26, - 20 - ], + "ShimSetting": [622, -7195, -8782, 671, 107, 20, -26, 20], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_epi.json index 660eb9b62..aee6b62b0 100644 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994527, - 0.100228, - 0.0294971, - -0.0861354, - 0.946352, - -0.311446 - ], + "ImageOrientationPatientDICOM": [0.994527, 0.100228, 0.0294971, -0.0861354, 0.946352, -0.311446], "ImageOrientationText": "Tra>Cor(-17.9)>Sag(3.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-01_ses-017_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 622, - -7195, - -8782, - 671, - 107, - 20, - -26, - 20 - ], + "ShimSetting": [622, -7195, -8782, 671, 107, 20, -26, 20], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_epi.json index 35ff1ad3a..bb512b886 100644 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994527, - 0.100228, - 0.0294971, - -0.0861354, - 0.946352, - -0.311446 - ], + "ImageOrientationPatientDICOM": [0.994527, 0.100228, 0.0294971, -0.0861354, 0.946352, -0.311446], "ImageOrientationText": "Tra>Cor(-17.9)>Sag(3.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-01_ses-017_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 622, - -7195, - -8782, - 671, - 107, - 20, - -26, - 20 - ], + "ShimSetting": [622, -7195, -8782, 671, 107, 20, -26, 20], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_epi.json index 5e7bdaca1..a2e235f38 100644 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994527, - 0.100228, - 0.0294971, - -0.0861354, - 0.946352, - -0.311446 - ], + "ImageOrientationPatientDICOM": [0.994527, 0.100228, 0.0294971, -0.0861354, 0.946352, -0.311446], "ImageOrientationText": "Tra>Cor(-17.9)>Sag(3.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-01_ses-017_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 622, - -7195, - -8782, - 671, - 107, - 20, - -26, - 20 - ], + "ShimSetting": [622, -7195, -8782, 671, 107, 20, -26, 20], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_epi.json b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_epi.json index 8cee9a27a..59de21b3c 100644 --- a/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-01/ses-017/fmap/sub-01_ses-017_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.994527, - 0.100228, - 0.0294971, - -0.0861354, - 0.946352, - -0.311446 - ], + "ImageOrientationPatientDICOM": [0.994527, 0.100228, 0.0294971, -0.0861354, 0.946352, -0.311446], "ImageOrientationText": "Tra>Cor(-17.9)>Sag(3.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-01_ses-017_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 622, - -7195, - -8782, - 671, - 107, - 20, - -26, - 20 - ], + "ShimSetting": [622, -7195, -8782, 671, 107, 20, -26, 20], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 03f04412b5e4a2dd9c08a500e8a1db5da6dff814 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:39:35 -0400 Subject: [PATCH 235/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-03_ses-003_acq-axial_localizer.json | 81 +++ .../sub-03_ses-003_acq-axial_localizer.nii.gz | 1 + .../sub-03_ses-003_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-003_acq-coronal_localizer.nii.gz | 1 + ...sub-03_ses-003_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-003_acq-sagittal_localizer.nii.gz | 1 + sub-03/ses-003/anat/sub-03_ses-003_scout.json | 542 ++++++++++++++++++ .../ses-003/anat/sub-03_ses-003_scout.nii.gz | 1 + ...3_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ...-003_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-01_part-mag_events.tsv | 1 + ...003_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-01_part-phase_events.tsv | 1 + ...3_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-003_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-02_part-mag_events.tsv | 1 + ...003_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-02_part-phase_events.tsv | 1 + ...3_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-003_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-03_part-mag_events.tsv | 1 + ...003_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-03_part-phase_events.tsv | 1 + ...3_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-003_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-04_part-mag_events.tsv | 1 + ...003_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-04_part-phase_events.tsv | 1 + ...3_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-003_task-mario3_run-05_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-05_part-mag_events.tsv | 1 + ...003_task-mario3_run-05_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-05_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-05_part-phase_events.tsv | 1 + ...3_task-mario3_run-05_part-phase_sbref.json | 153 +++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + sub-03/ses-003/sub-03_ses-003_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 93 files changed, 6371 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-003/anat/sub-03_ses-003_acq-axial_localizer.json create mode 120000 sub-03/ses-003/anat/sub-03_ses-003_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-003/anat/sub-03_ses-003_acq-coronal_localizer.json create mode 120000 sub-03/ses-003/anat/sub-03_ses-003_acq-coronal_localizer.nii.gz create mode 100644 sub-03/ses-003/anat/sub-03_ses-003_acq-sagittal_localizer.json create mode 120000 sub-03/ses-003/anat/sub-03_ses-003_acq-sagittal_localizer.nii.gz create mode 100644 sub-03/ses-003/anat/sub-03_ses-003_scout.json create mode 120000 sub-03/ses-003/anat/sub-03_ses-003_scout.nii.gz create mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_part-mag_epi.json create mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz create mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.json create mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_part-mag_bold.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_part-mag_bold.nii.gz create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_part-mag_events.tsv create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_part-mag_sbref.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_part-phase_bold.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_part-phase_bold.nii.gz create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_part-phase_events.tsv create mode 100644 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_part-phase_sbref.json create mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_part-phase_sbref.nii.gz create mode 120000 sub-03/ses-003/sub-03_ses-003_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index a9d93d359..84fafac87 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit a9d93d35925f307786dc5bb3727fa2c45935afb2 +Subproject commit 84fafac872d7f2bfa401045a2e599c7beb340994 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-03/ses-003/anat/sub-03_ses-003_acq-axial_localizer.json b/sub-03/ses-003/anat/sub-03_ses-003_acq-axial_localizer.json new file mode 100644 index 000000000..f7fced81a --- /dev/null +++ b/sub-03/ses-003/anat/sub-03_ses-003_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:11:8.087500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + 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a/sub-03/ses-003/anat/sub-03_ses-003_acq-sagittal_localizer.json b/sub-03/ses-003/anat/sub-03_ses-003_acq-sagittal_localizer.json new file mode 100644 index 000000000..3f7076303 --- /dev/null +++ b/sub-03/ses-003/anat/sub-03_ses-003_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:11:1.097500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 0, + 1, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Sag", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + 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+../../.git/annex/objects/Gf/wk/MD5E-s3911--4fa90461cf7f535c1344b65e47d0c0ad.tsv/MD5E-s3911--4fa90461cf7f535c1344b65e47d0c0ad.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..c060ba650 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": 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"ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0782892, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [637, -7218, -8755, 684, 37, -30, 50, 0], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 271.349, + "dcmmeta_affine": [ + [-1.9998747110366821, 0.022339828312397003, 0.001458634389564395, 108.00880432128906], + [0.021111981943249702, 1.9252887964248657, -0.5411258339881897, -74.38045501708984], + [0.007448475807905197, 0.5410765409469604, 1.9254039525985718, -53.165042877197266], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From d40c55cdb0ce7bc7d09cc73b23e7fe4cf1460455 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:39:58 -0400 Subject: [PATCH 236/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..fa751c3f1 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = e5a5a708-674f-4e13-a840-c622ad57f7b6 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..8168e7575 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 8168e7575894101551c619a485e4149f99d8ad57 From 5d64e4414fc84b834c5c7718ee4ed2d40e3a3347 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:40:13 -0400 Subject: [PATCH 237/463] fix fmap phase --- ...3_ses-003_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-003_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-003_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - sub-03/ses-003/sub-03_ses-003_scans.tsv | 2 +- 29 files changed, 1 insertion(+), 1097 deletions(-) rename sub-03/ses-003/fmap/{sub-03_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-003_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-003/fmap/{sub-03_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-003_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-003/fmap/{sub-03_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-003_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-003/fmap/{sub-03_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-003_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-003/fmap/{sub-03_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-003_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-003/fmap/{sub-03_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-003_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-003/fmap/{sub-03_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-003_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-003/fmap/{sub-03_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-003_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-03/ses-003/fmap/{sub-03_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-03_ses-003_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-03/ses-003/fmap/{sub-03_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-03_ses-003_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-03/ses-003/fmap/{sub-03_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-03_ses-003_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-03/ses-003/fmap/{sub-03_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-03_ses-003_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-03/ses-003/fmap/{sub-03_ses-003_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-03_ses-003_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-03/ses-003/fmap/{sub-03_ses-003_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-03_ses-003_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 61790024e..000000000 --- a/sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:12:8.852500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999937, -0.010556, 0.00372424, 0.0111699, 0.962644, -0.270538], - "ImageOrientationText": 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0.06243591120635, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "181255.343000", - "SliceLocation": -30.978728152412, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999584187, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "181017.539000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["181208.852500", "181210.342500", "181211.832500"], - "ContentTime": ["181255.345000", "181255.348000", "181255.350000"], - "InstanceCreationTime": ["181255.345000", "181255.348000", "181255.350000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4830.0, 4830.0, 4828.0], - "WindowWidth": [18588.0, 18586.0, 18592.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 39302f4e0..000000000 --- a/sub-03/ses-003/fmap/sub-03_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/m1/V1/MD5E-s3334445--f357c8980be32708614f254753346d12.nii.gz/MD5E-s3334445--f357c8980be32708614f254753346d12.nii.gz \ No newline at end of file diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 0205904cd..000000000 --- a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:11:58.422500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999937, - -0.010556, - 0.00372424, - 0.0111699, - 0.962644, - -0.270538 - ], - "ImageOrientationText": "Tra>Cor(-15.7)>Sag(0.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0624359, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 637, - -7218, - -8755, - 684, - 37, - -30, - 50, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 271.349, - "WipMemBlock": "47e0a14b-11c9-44ab-b895-12333ff8e0a1||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 682935297..000000000 --- a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/15/mz/MD5E-s1112216--1aca974b630c4e9e187677df95d22a55.nii.gz/MD5E-s1112216--1aca974b630c4e9e187677df95d22a55.nii.gz \ No newline at end of file diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index a5c71ff16..000000000 --- a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:13:13.080000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999937, - -0.010556, - 0.00372424, - 0.0111699, - 0.962644, - -0.270538 - ], - "ImageOrientationText": "Tra>Cor(-15.7)>Sag(0.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0782892, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 637, - -7218, - -8755, - 684, - 37, - -30, - 50, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 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-../../../.git/annex/objects/V9/k4/MD5E-s1103719--98d0f35231994be96e2133e607f55fa6.nii.gz/MD5E-s1103719--98d0f35231994be96e2133e607f55fa6.nii.gz \ No newline at end of file diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 6b1013067..000000000 --- a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:21:44.860000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 9b324c55f..000000000 --- a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:40:22.322500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of 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b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 2c27fd2b7..000000000 --- a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/J5/Xw/MD5E-s1103727--8689cf14b884be8636a48a34ccc6165c.nii.gz/MD5E-s1103727--8689cf14b884be8636a48a34ccc6165c.nii.gz \ No newline at end of file diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index 155308a8e..000000000 --- a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:49:10.315000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999937, - -0.010556, - 0.00372424, - 0.0111699, - 0.962644, - -0.270538 - ], - "ImageOrientationText": "Tra>Cor(-15.7)>Sag(0.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-05", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0782892, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 637, - -7218, - -8755, - 684, - 37, - -30, - 50, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 271.349, - "WipMemBlock": "7d0a9612-64f3-49f2-b088-664a31302ad1||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index 41d2f5fbb..000000000 --- a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/xM/Xx/MD5E-s1103750--54522313f141362afa31522f618a8aa2.nii.gz/MD5E-s1103750--54522313f141362afa31522f618a8aa2.nii.gz \ No newline at end of file diff --git a/sub-03/ses-003/sub-03_ses-003_scans.tsv b/sub-03/ses-003/sub-03_ses-003_scans.tsv index cd03235f8..1d77e102c 120000 --- a/sub-03/ses-003/sub-03_ses-003_scans.tsv +++ b/sub-03/ses-003/sub-03_ses-003_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/Gf/wk/MD5E-s3911--4fa90461cf7f535c1344b65e47d0c0ad.tsv/MD5E-s3911--4fa90461cf7f535c1344b65e47d0c0ad.tsv \ No newline at end of file +../../.git/annex/objects/PP/p3/MD5E-s3068--ea7df97b68803effd87cde7d9cb2bf67.tsv/MD5E-s3068--ea7df97b68803effd87cde7d9cb2bf67.tsv \ No newline at end of file From 61a4240d9c0ad3b4eb2bd03cbdf4b8310d04b143 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:40:22 -0400 Subject: [PATCH 238/463] fix complex event files --- ...g_events.tsv => sub-03_ses-003_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-03_ses-003_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-03_ses-003_task-mario3_run-03_events.tsv} | 0 .../func/sub-03_ses-003_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-03_ses-003_task-mario3_run-04_events.tsv} | 0 .../func/sub-03_ses-003_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-03_ses-003_task-mario3_run-04_part-phase_events.tsv | 1 - ...g_events.tsv => sub-03_ses-003_task-mario3_run-05_events.tsv} | 0 .../func/sub-03_ses-003_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-03_ses-003_task-mario3_run-05_part-phase_events.tsv | 1 - 10 files changed, 5 deletions(-) rename sub-03/ses-003/func/{sub-03_ses-003_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-003_task-mario3_run-01_events.tsv} (100%) rename sub-03/ses-003/func/{sub-03_ses-003_task-mario3_run-01_part-phase_events.tsv => sub-03_ses-003_task-mario3_run-02_events.tsv} (100%) rename sub-03/ses-003/func/{sub-03_ses-003_task-mario3_run-02_part-mag_events.tsv => sub-03_ses-003_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-03_part-phase_events.tsv rename sub-03/ses-003/func/{sub-03_ses-003_task-mario3_run-02_part-phase_events.tsv => sub-03_ses-003_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_part-phase_events.tsv rename sub-03/ses-003/func/{sub-03_ses-003_task-mario3_run-03_part-mag_events.tsv => sub-03_ses-003_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_part-phase_events.tsv diff --git a/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-02_events.tsv similarity index 100% rename from sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-01_part-phase_events.tsv rename to sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-02_events.tsv diff --git a/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-02_part-mag_events.tsv b/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-03_events.tsv similarity index 100% rename from sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-02_part-mag_events.tsv rename to sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-03_events.tsv diff --git a/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-03_part-phase_events.tsv b/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-02_part-phase_events.tsv b/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_events.tsv similarity index 100% rename from sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-02_part-phase_events.tsv rename to sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_events.tsv diff --git a/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_part-mag_events.tsv b/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_part-phase_events.tsv b/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-03_part-mag_events.tsv b/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_events.tsv similarity index 100% rename from sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-03_part-mag_events.tsv rename to sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_events.tsv diff --git a/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_part-mag_events.tsv b/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_part-phase_events.tsv b/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-003/func/sub-03_ses-003_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From b827aa0faf1ac80d1e4159f97977093832e7cf14 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:41:31 -0400 Subject: [PATCH 239/463] fill IntendedFor --- ...3_ses-003_acq-sbref_dir-AP_run-01_epi.json | 92 +++---------------- ...3_ses-003_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...3_ses-003_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...3_ses-003_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...3_ses-003_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- ...3_ses-003_acq-sbref_dir-PA_run-05_epi.json | 88 ++---------------- 6 files changed, 46 insertions(+), 486 deletions(-) diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_epi.json index 56cf28f09..2e6957f25 100644 --- a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999937, - -0.010556, - 0.00372424, - 0.0111699, - 0.962644, - -0.270538 - ], + "ImageOrientationPatientDICOM": [0.999937, -0.010556, 0.00372424, 0.0111699, 0.962644, -0.270538], "ImageOrientationText": "Tra>Cor(-15.7)>Sag(0.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,19 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-03_ses-003_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-003/func/sub-03_ses-003_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-003/func/sub-03_ses-003_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-003/func/sub-03_ses-003_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-003/func/sub-03_ses-003_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +67,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 637, - -7218, - -8755, - 684, - 37, - -30, - 50, - 0 - ], + "ShimSetting": [637, -7218, -8755, 684, 37, -30, 50, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_epi.json b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_epi.json index d04112e5e..a06eeeeca 100644 --- a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999937, - -0.010556, - 0.00372424, - 0.0111699, - 0.962644, - -0.270538 - ], + "ImageOrientationPatientDICOM": [0.999937, -0.010556, 0.00372424, 0.0111699, 0.962644, -0.270538], "ImageOrientationText": "Tra>Cor(-15.7)>Sag(0.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-03_ses-003_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 637, - -7218, - -8755, - 684, - 37, - -30, - 50, - 0 - ], + "ShimSetting": [637, -7218, -8755, 684, 37, -30, 50, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_epi.json b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_epi.json index 0a1466347..710609935 100644 --- a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999937, - -0.010556, - 0.00372424, - 0.0111699, - 0.962644, - -0.270538 - ], + "ImageOrientationPatientDICOM": [0.999937, -0.010556, 0.00372424, 0.0111699, 0.962644, -0.270538], "ImageOrientationText": "Tra>Cor(-15.7)>Sag(0.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-03_ses-003_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 637, - -7218, - -8755, - 684, - 37, - -30, - 50, - 0 - ], + "ShimSetting": [637, -7218, -8755, 684, 37, -30, 50, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-03_epi.json b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-03_epi.json index d27d7c499..4c0a6d95c 100644 --- a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999937, - -0.010556, - 0.00372424, - 0.0111699, - 0.962644, - -0.270538 - ], + "ImageOrientationPatientDICOM": [0.999937, -0.010556, 0.00372424, 0.0111699, 0.962644, -0.270538], "ImageOrientationText": "Tra>Cor(-15.7)>Sag(0.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-03_ses-003_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 637, - -7218, - -8755, - 684, - 37, - -30, - 50, - 0 - ], + "ShimSetting": [637, -7218, -8755, 684, 37, -30, 50, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_epi.json b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_epi.json index db54655b2..18d0a0c5a 100644 --- a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999937, - -0.010556, - 0.00372424, - 0.0111699, - 0.962644, - -0.270538 - ], + "ImageOrientationPatientDICOM": [0.999937, -0.010556, 0.00372424, 0.0111699, 0.962644, -0.270538], "ImageOrientationText": "Tra>Cor(-15.7)>Sag(0.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-03_ses-003_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 637, - -7218, - -8755, - 684, - 37, - -30, - 50, - 0 - ], + "ShimSetting": [637, -7218, -8755, 684, 37, -30, 50, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_epi.json b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_epi.json index 1794448a5..68cbeee3f 100644 --- a/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-03/ses-003/fmap/sub-03_ses-003_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999937, - -0.010556, - 0.00372424, - 0.0111699, - 0.962644, - -0.270538 - ], + "ImageOrientationPatientDICOM": [0.999937, -0.010556, 0.00372424, 0.0111699, 0.962644, -0.270538], "ImageOrientationText": "Tra>Cor(-15.7)>Sag(0.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-03_ses-003_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 637, - -7218, - -8755, - 684, - 37, - -30, - 50, - 0 - ], + "ShimSetting": [637, -7218, -8755, 684, 37, -30, 50, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.4875, 0.5875, 0.685, 0.7825, 0.88, 0.9775, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.485, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 3d6d22884786341fbacffe4c6b0fa1ffa27ee067 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:42:07 -0400 Subject: [PATCH 240/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..9bcb14add --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 7177247d-bb48-489a-9ff8-b40d3e672cdb diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..ebb5f3bf1 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit ebb5f3bf13dc44b8fe83742011846965c2fbc2c0 From c7de23aacda2b32b6e1041639154da7107c69c18 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:42:34 -0400 Subject: [PATCH 241/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..777a4648d --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 78e302b9-760a-4f04-b38e-ac723c48b0b4 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..6d8c7a6ee --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 6d8c7a6ee4a143c9feab79a9736cf3bc0837d9ef From b632038f17e2a6c16091030c76d2c9fefe6fe8a6 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:45:51 -0400 Subject: [PATCH 242/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..b95b14850 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = f9f1f10d-b2c6-4224-9841-c9ed16d01e3a diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..5a76708c4 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 5a76708c44dbc21b8c0d21c3c4947bd53ea36265 From bf068b914cff9cfcb66018169e69f6b76eb2b68f Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:46:25 -0400 Subject: [PATCH 243/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-06_ses-002_acq-axial_localizer.json | 81 +++ .../sub-06_ses-002_acq-axial_localizer.nii.gz | 1 + .../sub-06_ses-002_acq-coronal_localizer.json | 81 +++ ...ub-06_ses-002_acq-coronal_localizer.nii.gz | 1 + ...sub-06_ses-002_acq-sagittal_localizer.json | 86 +++ ...b-06_ses-002_acq-sagittal_localizer.nii.gz | 1 + sub-06/ses-002/anat/sub-06_ses-002_scout.json | 542 ++++++++++++++++++ .../ses-002/anat/sub-06_ses-002_scout.nii.gz | 1 + ...2_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-002_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-01_part-mag_events.tsv | 1 + ...002_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-01_part-phase_events.tsv | 1 + ...2_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-002_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-02_part-mag_events.tsv | 1 + ...002_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-02_part-phase_events.tsv | 1 + ...2_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-002_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-03_part-mag_events.tsv | 1 + ...002_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-03_part-phase_events.tsv | 1 + ...2_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-002_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-04_part-mag_events.tsv | 1 + ...002_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-04_part-phase_events.tsv | 1 + ...2_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-06/ses-002/sub-06_ses-002_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5409 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-06/ses-002/anat/sub-06_ses-002_acq-axial_localizer.json create mode 120000 sub-06/ses-002/anat/sub-06_ses-002_acq-axial_localizer.nii.gz create mode 100644 sub-06/ses-002/anat/sub-06_ses-002_acq-coronal_localizer.json create mode 120000 sub-06/ses-002/anat/sub-06_ses-002_acq-coronal_localizer.nii.gz create mode 100644 sub-06/ses-002/anat/sub-06_ses-002_acq-sagittal_localizer.json create mode 120000 sub-06/ses-002/anat/sub-06_ses-002_acq-sagittal_localizer.nii.gz create mode 100644 sub-06/ses-002/anat/sub-06_ses-002_scout.json create mode 120000 sub-06/ses-002/anat/sub-06_ses-002_scout.nii.gz create mode 100644 sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_part-phase_sbref.nii.gz create mode 120000 sub-06/ses-002/sub-06_ses-002_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 5a76708c4..548794c63 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 5a76708c44dbc21b8c0d21c3c4947bd53ea36265 +Subproject commit 548794c631f6cc4fc14d629456d6ac39a8b34d4d diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..db37a3f34 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-06 41 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-06/ses-002/anat/sub-06_ses-002_acq-axial_localizer.json b/sub-06/ses-002/anat/sub-06_ses-002_acq-axial_localizer.json new file mode 100644 index 000000000..c9b97df00 --- /dev/null +++ b/sub-06/ses-002/anat/sub-06_ses-002_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:38:45.097500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0289626, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 230.874 +} \ No newline at end of file diff --git a/sub-06/ses-002/anat/sub-06_ses-002_acq-axial_localizer.nii.gz b/sub-06/ses-002/anat/sub-06_ses-002_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..bc4f41343 --- /dev/null +++ b/sub-06/ses-002/anat/sub-06_ses-002_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Xj/Pw/MD5E-s165314--d24ddaf13c6ffa8367f2ff97e7880602.nii.gz/MD5E-s165314--d24ddaf13c6ffa8367f2ff97e7880602.nii.gz \ No newline at end of file diff --git a/sub-06/ses-002/anat/sub-06_ses-002_acq-coronal_localizer.json b/sub-06/ses-002/anat/sub-06_ses-002_acq-coronal_localizer.json new file mode 100644 index 000000000..ea999bd92 --- /dev/null +++ b/sub-06/ses-002/anat/sub-06_ses-002_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:38:52.087500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", 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.../sub-03_ses-005_acq-axial_localizer.json | 81 +++ .../sub-03_ses-005_acq-axial_localizer.nii.gz | 1 + .../sub-03_ses-005_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-005_acq-coronal_localizer.nii.gz | 1 + ...sub-03_ses-005_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-005_acq-sagittal_localizer.nii.gz | 1 + sub-03/ses-005/anat/sub-03_ses-005_scout.json | 542 ++++++++++++++++++ .../ses-005/anat/sub-03_ses-005_scout.nii.gz | 1 + ...5_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ...-005_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...05_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...005_task-mario3_run-01_part-mag_events.tsv | 1 + ...005_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...05_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-01_part-phase_events.tsv | 1 + ...5_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-005_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...05_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...005_task-mario3_run-02_part-mag_events.tsv | 1 + ...005_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...05_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-02_part-phase_events.tsv | 1 + ...5_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-005_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...05_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...005_task-mario3_run-03_part-mag_events.tsv | 1 + ...005_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...05_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-03_part-phase_events.tsv | 1 + ...5_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-005_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...05_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...k-mario3_run-04_part-mag_bold__dup-01.json | 172 ++++++ ...mario3_run-04_part-mag_bold__dup-01.nii.gz | 1 + ...005_task-mario3_run-04_part-mag_events.tsv | 1 + ...005_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...05_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...mario3_run-04_part-phase_bold__dup-01.json | 178 ++++++ ...rio3_run-04_part-phase_bold__dup-01.nii.gz | 1 + ...5_task-mario3_run-04_part-phase_events.tsv | 1 + ...5_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-mario3_run-04_sbref__part-mag_dup-01.json | 150 +++++ ...ario3_run-04_sbref__part-mag_dup-01.nii.gz | 1 + ...ario3_run-04_sbref__part-phase_dup-01.json | 153 +++++ ...io3_run-04_sbref__part-phase_dup-01.nii.gz | 1 + sub-03/ses-005/sub-03_ses-005_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 91 files changed, 6369 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-005/anat/sub-03_ses-005_acq-axial_localizer.json create mode 120000 sub-03/ses-005/anat/sub-03_ses-005_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-005/anat/sub-03_ses-005_acq-coronal_localizer.json create mode 120000 sub-03/ses-005/anat/sub-03_ses-005_acq-coronal_localizer.nii.gz create mode 100644 sub-03/ses-005/anat/sub-03_ses-005_acq-sagittal_localizer.json create mode 120000 sub-03/ses-005/anat/sub-03_ses-005_acq-sagittal_localizer.nii.gz create mode 100644 sub-03/ses-005/anat/sub-03_ses-005_scout.json create mode 120000 sub-03/ses-005/anat/sub-03_ses-005_scout.nii.gz create mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_part-mag_epi.json create mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz create mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_part-phase_epi.json create mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-mag_bold.nii.gz create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-mag_bold__dup-01.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-mag_bold__dup-01.nii.gz create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-phase_bold.nii.gz create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-phase_bold__dup-01.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-phase_bold__dup-01.nii.gz create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_sbref__part-mag_dup-01.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_sbref__part-mag_dup-01.nii.gz create mode 100644 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_sbref__part-phase_dup-01.json create mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_sbref__part-phase_dup-01.nii.gz create mode 120000 sub-03/ses-005/sub-03_ses-005_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 8f495782a..7976f6276 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 8f495782a70b9cc5331d47833247d080de7276fa +Subproject commit 7976f6276f434206395cd8399b4f467a518fb449 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-03/ses-005/anat/sub-03_ses-005_acq-axial_localizer.json b/sub-03/ses-005/anat/sub-03_ses-005_acq-axial_localizer.json new file mode 100644 index 000000000..0b9967de2 --- /dev/null +++ b/sub-03/ses-005/anat/sub-03_ses-005_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:03:16.040000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.261, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0371491, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 232.555 +} \ No newline at end of file diff --git a/sub-03/ses-005/anat/sub-03_ses-005_acq-axial_localizer.nii.gz b/sub-03/ses-005/anat/sub-03_ses-005_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..93e463f0d --- /dev/null +++ b/sub-03/ses-005/anat/sub-03_ses-005_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/8w/Gm/MD5E-s166313--be6313e5a47cb8e8598a34359177af5c.nii.gz/MD5E-s166313--be6313e5a47cb8e8598a34359177af5c.nii.gz \ No newline at end of file diff --git a/sub-03/ses-005/anat/sub-03_ses-005_acq-coronal_localizer.json b/sub-03/ses-005/anat/sub-03_ses-005_acq-coronal_localizer.json new file mode 100644 index 000000000..9175dd12c --- /dev/null +++ b/sub-03/ses-005/anat/sub-03_ses-005_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:03:23.030000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.261, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": 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-53.416873931884766], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 6235f09f9662a9885ffc2f90d53258efcb8927fd Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:46:35 -0400 Subject: [PATCH 245/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..12fe52efd --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 6e52d8f5-77b4-427f-9bd3-d44fb8919dd3 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..0818d94c6 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 0818d94c63805dccfbf7e13214746a0a9d3d21f9 From 530774a07e906ec4abb7f4768f64fbf29e6949ae Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:46:42 -0400 Subject: [PATCH 246/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-016_acq-axial_localizer.json | 81 +++ .../sub-02_ses-016_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-016_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-016_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-016_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-016_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-016/anat/sub-02_ses-016_scout.json | 542 ++++++++++++++++++ .../ses-016/anat/sub-02_ses-016_scout.nii.gz | 1 + ...6_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ...-016_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...16_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...016_task-mario3_run-01_part-mag_events.tsv | 1 + ...016_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...16_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-01_part-phase_events.tsv | 1 + ...6_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-016_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...16_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...016_task-mario3_run-02_part-mag_events.tsv | 1 + ...016_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...16_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-02_part-phase_events.tsv | 1 + ...6_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-016_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...16_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...016_task-mario3_run-03_part-mag_events.tsv | 1 + ...016_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...16_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-03_part-phase_events.tsv | 1 + ...6_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-016_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...16_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...016_task-mario3_run-04_part-mag_events.tsv | 1 + ...016_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...16_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-04_part-phase_events.tsv | 1 + ...6_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-016_task-mario3_run-05_part-mag_bold.json | 172 ++++++ ...16_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...016_task-mario3_run-05_part-mag_events.tsv | 1 + ...016_task-mario3_run-05_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...16_task-mario3_run-05_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-05_part-phase_events.tsv | 1 + ...6_task-mario3_run-05_part-phase_sbref.json | 153 +++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + sub-02/ses-016/sub-02_ses-016_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 93 files changed, 6371 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-016/anat/sub-02_ses-016_acq-axial_localizer.json create mode 120000 sub-02/ses-016/anat/sub-02_ses-016_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-016/anat/sub-02_ses-016_acq-coronal_localizer.json create mode 120000 sub-02/ses-016/anat/sub-02_ses-016_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-016/anat/sub-02_ses-016_acq-sagittal_localizer.json create mode 120000 sub-02/ses-016/anat/sub-02_ses-016_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-016/anat/sub-02_ses-016_scout.json create mode 120000 sub-02/ses-016/anat/sub-02_ses-016_scout.nii.gz create mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_part-mag_epi.json create mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz create mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_part-phase_epi.json create mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_part-mag_bold.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_part-mag_bold.nii.gz create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_part-mag_events.tsv create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_part-mag_sbref.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_part-phase_bold.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_part-phase_bold.nii.gz create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_part-phase_events.tsv create mode 100644 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_part-phase_sbref.json create mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_part-phase_sbref.nii.gz create mode 120000 sub-02/ses-016/sub-02_ses-016_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 22df60cac..ee7889213 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 22df60cacb170a726b40372fd1f4e1b14cbba088 +Subproject commit ee788921348bbbeae7b3411fcc84c9190dbd19dd diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..83ada7a9d --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 51 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-016/anat/sub-02_ses-016_acq-axial_localizer.json b/sub-02/ses-016/anat/sub-02_ses-016_acq-axial_localizer.json new file mode 100644 index 000000000..d9dcfd591 --- /dev/null +++ b/sub-02/ses-016/anat/sub-02_ses-016_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:10:23.040000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0477507, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 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newline at end of file diff --git a/sub-02/ses-016/anat/sub-02_ses-016_acq-coronal_localizer.nii.gz b/sub-02/ses-016/anat/sub-02_ses-016_acq-coronal_localizer.nii.gz new file mode 120000 index 000000000..14a78f1c2 --- /dev/null +++ b/sub-02/ses-016/anat/sub-02_ses-016_acq-coronal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/f9/VJ/MD5E-s194184--c61ee73c6d32782185ef1e1b406f0ddf.nii.gz/MD5E-s194184--c61ee73c6d32782185ef1e1b406f0ddf.nii.gz \ No newline at end of file diff --git a/sub-02/ses-016/anat/sub-02_ses-016_acq-sagittal_localizer.json b/sub-02/ses-016/anat/sub-02_ses-016_acq-sagittal_localizer.json new file mode 100644 index 000000000..e8184c0bb --- /dev/null +++ b/sub-02/ses-016/anat/sub-02_ses-016_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:10:16.050000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": 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"TxRefAmp": 301.694, + "dcmmeta_affine": [ + [-1.9966061115264893, 0.029971018433570862, 0.11254291981458664, 103.28376007080078], + [-0.030039407312870026, 1.7347278594970703, -0.994895339012146, -49.20748519897461], + [0.11252468079328537, 0.9948974251747131, 1.7313339710235596, -98.86970520019531], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From b95f3a318803e952c210c93069cf60618d8bfec0 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:46:57 -0400 Subject: [PATCH 247/463] fix fmap phase --- ...6_ses-002_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-002_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-002_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-06/ses-002/sub-06_ses-002_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-06/ses-002/fmap/{sub-06_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-06_ses-002_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-002/fmap/{sub-06_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-002_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-002/fmap/{sub-06_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-06_ses-002_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-002/fmap/{sub-06_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-002_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-002/fmap/{sub-06_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-06_ses-002_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-06/ses-002/fmap/{sub-06_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-06_ses-002_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-06/ses-002/fmap/{sub-06_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-06_ses-002_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-06/ses-002/fmap/{sub-06_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-06_ses-002_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-06/ses-002/fmap/{sub-06_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-06_ses-002_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-06/ses-002/fmap/{sub-06_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-06_ses-002_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-06/ses-002/fmap/{sub-06_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-06_ses-002_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-06/ses-002/fmap/{sub-06_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-06_ses-002_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index ad98339f6..000000000 --- a/sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:40:18.247500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - 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["154103.855000", "154103.857000", "154103.860000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4828.0, 4804.0, 4804.0], - "WindowWidth": [18574.0, 18546.0, 18550.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 9cc8c71b9..000000000 --- a/sub-06/ses-002/fmap/sub-06_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Wz/2X/MD5E-s3335114--3f60c72c6e67d5eff4ae79dd09ba2566.nii.gz/MD5E-s3335114--3f60c72c6e67d5eff4ae79dd09ba2566.nii.gz \ No newline at end of file diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 3520df3cd..000000000 --- a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:40:7.817500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998782, - -0.0490697, - 0.0051772, - 0.0476255, - 0.93128, - -0.361179 - ], - "ImageOrientationText": "Tra>Cor(-21.2)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - 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a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 25309baf1..000000000 --- a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/vK/xj/MD5E-s1112073--a239c606a1ee73e3ecbc2b0b6176d9b8.nii.gz/MD5E-s1112073--a239c606a1ee73e3ecbc2b0b6176d9b8.nii.gz \ No newline at end of file diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 471a5c699..000000000 --- a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:41:58.072500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - 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1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 230.874, - "WipMemBlock": "9ea76d6f-fa78-4e60-8f69-4ce5e5952af4||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index a208ee6d7..000000000 --- a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/f7/k8/MD5E-s1103609--da5d1a913e33ed57abf7f86b42477377.nii.gz/MD5E-s1103609--da5d1a913e33ed57abf7f86b42477377.nii.gz \ No newline at end of file diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index d055cdfc0..000000000 --- a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:51:10.515000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998782, - -0.0490697, - 0.0051772, - 0.0476255, - 0.93128, - -0.361179 - ], - "ImageOrientationText": "Tra>Cor(-21.2)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0426591, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 623, - -7253, - -8836, - 529, - -3, - -226, - -107, - -9 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 230.874, - "WipMemBlock": "6d815a2d-40e9-4b7b-b902-734d3b6edd09||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 5aee7269e..000000000 --- a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/7k/jp/MD5E-s1103513--80446f237addad4895e594d497fb88a2.nii.gz/MD5E-s1103513--80446f237addad4895e594d497fb88a2.nii.gz \ No newline at end of file diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index b5691ca34..000000000 --- a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:01:1.935000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998782, - -0.0490697, - 0.0051772, - 0.0476255, - 0.93128, - -0.361179 - ], - "ImageOrientationText": "Tra>Cor(-21.2)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0426591, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 623, - -7253, - -8836, - 529, - -3, - -226, - -107, - -9 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 230.874, - "WipMemBlock": "177854bf-ca3b-4d4a-85db-9b2f57c5d965||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 6828bd8cc..000000000 --- a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/09/m6/MD5E-s1103459--b43c230da0f93b19160e3fcd5f589843.nii.gz/MD5E-s1103459--b43c230da0f93b19160e3fcd5f589843.nii.gz \ No newline at end of file diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 5106ce367..000000000 --- a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:10:17.337500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998782, - -0.0490697, - 0.0051772, - 0.0476255, - 0.93128, - -0.361179 - ], - "ImageOrientationText": "Tra>Cor(-21.2)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0426591, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 623, - -7253, - -8836, - 529, - -3, - -226, - -107, - -9 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 230.874, - "WipMemBlock": "a474a4b8-a4c7-4723-8c46-1f86428d12ba||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 5561a2906..000000000 --- a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/9x/6W/MD5E-s1103619--d6718e3c4606c4205e434d4391dff2f3.nii.gz/MD5E-s1103619--d6718e3c4606c4205e434d4391dff2f3.nii.gz \ No newline at end of file diff --git a/sub-06/ses-002/sub-06_ses-002_scans.tsv b/sub-06/ses-002/sub-06_ses-002_scans.tsv index 8584eb796..eda1c0131 120000 --- a/sub-06/ses-002/sub-06_ses-002_scans.tsv +++ b/sub-06/ses-002/sub-06_ses-002_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/w7/v9/MD5E-s3289--59e28813803e9a34066cbc3a50948680.tsv/MD5E-s3289--59e28813803e9a34066cbc3a50948680.tsv \ No newline at end of file +../../.git/annex/objects/K4/jm/MD5E-s2567--495be9fbf3038c2c9c41726dfcabae4a.tsv/MD5E-s2567--495be9fbf3038c2c9c41726dfcabae4a.tsv \ No newline at end of file From ee6affeb35de3e8a4b57b5fe42660d2188f39d0b Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:47:00 -0400 Subject: [PATCH 248/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-06_ses-004_acq-axial_localizer.json | 81 +++ .../sub-06_ses-004_acq-axial_localizer.nii.gz | 1 + .../sub-06_ses-004_acq-coronal_localizer.json | 81 +++ ...ub-06_ses-004_acq-coronal_localizer.nii.gz | 1 + ...sub-06_ses-004_acq-sagittal_localizer.json | 86 +++ ...b-06_ses-004_acq-sagittal_localizer.nii.gz | 1 + sub-06/ses-004/anat/sub-06_ses-004_scout.json | 542 ++++++++++++++++++ .../ses-004/anat/sub-06_ses-004_scout.nii.gz | 1 + ...4_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-004_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...04_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...004_task-mario3_run-01_part-mag_events.tsv | 1 + ...004_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...04_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-01_part-phase_events.tsv | 1 + ...4_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-004_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...04_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...004_task-mario3_run-02_part-mag_events.tsv | 1 + ...004_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...04_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-02_part-phase_events.tsv | 1 + ...4_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-004_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...04_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...004_task-mario3_run-03_part-mag_events.tsv | 1 + ...004_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...04_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-03_part-phase_events.tsv | 1 + ...4_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-06/ses-004/sub-06_ses-004_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-06/ses-004/anat/sub-06_ses-004_acq-axial_localizer.json create mode 120000 sub-06/ses-004/anat/sub-06_ses-004_acq-axial_localizer.nii.gz create mode 100644 sub-06/ses-004/anat/sub-06_ses-004_acq-coronal_localizer.json create mode 120000 sub-06/ses-004/anat/sub-06_ses-004_acq-coronal_localizer.nii.gz create mode 100644 sub-06/ses-004/anat/sub-06_ses-004_acq-sagittal_localizer.json create mode 120000 sub-06/ses-004/anat/sub-06_ses-004_acq-sagittal_localizer.nii.gz create mode 100644 sub-06/ses-004/anat/sub-06_ses-004_scout.json create mode 120000 sub-06/ses-004/anat/sub-06_ses-004_scout.nii.gz create mode 100644 sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-06/ses-004/sub-06_ses-004_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 0818d94c6..bf035ab0f 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 0818d94c63805dccfbf7e13214746a0a9d3d21f9 +Subproject commit bf035ab0f6813fb6043aafa15c3498b05b22f01e diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..db37a3f34 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-06 41 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-06/ses-004/anat/sub-06_ses-004_acq-axial_localizer.json b/sub-06/ses-004/anat/sub-06_ses-004_acq-axial_localizer.json new file mode 100644 index 000000000..bf02c6f4e --- /dev/null +++ b/sub-06/ses-004/anat/sub-06_ses-004_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:56:8.077500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0287471, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 232.326 +} \ No newline at end of file diff --git a/sub-06/ses-004/anat/sub-06_ses-004_acq-axial_localizer.nii.gz b/sub-06/ses-004/anat/sub-06_ses-004_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..a0a7841ff --- /dev/null +++ b/sub-06/ses-004/anat/sub-06_ses-004_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/5k/P9/MD5E-s162452--79c1dd1ced38ea37721bc0b6e525c690.nii.gz/MD5E-s162452--79c1dd1ced38ea37721bc0b6e525c690.nii.gz \ No newline at end of file diff --git a/sub-06/ses-004/anat/sub-06_ses-004_acq-coronal_localizer.json b/sub-06/ses-004/anat/sub-06_ses-004_acq-coronal_localizer.json new file mode 100644 index 000000000..950a4c43d --- /dev/null +++ b/sub-06/ses-004/anat/sub-06_ses-004_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:56:15.067500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + 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+../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-phase_sbref.json b/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-phase_sbref.json new file mode 100644 index 000000000..074993654 --- /dev/null +++ b/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-phase_sbref.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:20:14.150000", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + 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"PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "func_task-mario3_run-03", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0423417, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "SeriesDescription": "func_task-mario3_run-03_SBRef", + "SeriesNumber": 15, + "ShimSetting": [ + 627, + -7249, + -8858, + 543, + 12, + -233, + -59, + -18 + ], + "SliceThickness": 2, + "SliceTiming": [ + 0, + 0.0975, + 0.195, + 0.2925, + 0.39, + 0.49, + 0.5875, + 0.685, + 0.7825, + 0.88, + 0.98, + 1.0775, + 1.175, + 1.2725, + 1.37, + 1.47, + 1.5675, + 1.665, + 1.7625, + 1.86, + 1.96, + 2.0575, + 2.155, + 2.2525, + 2.35, + 2.45, + 2.5475, + 2.645, + 2.7425, + 2.84, + 2.9375, + 3.0375, + 3.135, + 3.2325, + 3.33, + 3.4275, + 3.5275, + 3.625, + 3.7225, + 3.82, + 3.9175, + 4.0175, + 4.115, + 4.2125, + 4.31, + 4.4075, + 4.5075, + 4.605, + 4.7025, + 4.8, + 4.8975, + 4.9975, + 5.095, + 5.1925, + 5.29, + 5.3875, + 5.4875, + 5.585, + 5.6825, + 5.78 + ], + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 232.326, + "WipMemBlock": "174f1cca-caf8-4e19-9339-cd0f2b8228f1||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-phase_sbref.nii.gz b/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-phase_sbref.nii.gz new file mode 120000 index 000000000..75746d84c --- /dev/null +++ b/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/5P/Xx/MD5E-s1103529--f06231d8fafb38dca78a39930aace024.nii.gz/MD5E-s1103529--f06231d8fafb38dca78a39930aace024.nii.gz \ No newline at end of file diff --git a/sub-06/ses-004/sub-06_ses-004_scans.tsv b/sub-06/ses-004/sub-06_ses-004_scans.tsv new file mode 120000 index 000000000..f8a177d7b --- /dev/null +++ b/sub-06/ses-004/sub-06_ses-004_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/VW/wm/MD5E-s2667--ca09ce94d072330eedc63788e2943808.tsv/MD5E-s2667--ca09ce94d072330eedc63788e2943808.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..886fbbe23 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999387, -0.0340653, 0.00806245, 0.0347248, 0.93554, -0.35151], + "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.3)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0423417, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [627, -7249, -8858, 543, 12, -233, -59, -18], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 232.326, + "dcmmeta_affine": [ + [-1.9987741708755493, 0.06944950670003891, -0.008863141760230064, 102.50920867919922], + [0.06813059002161026, 1.871079444885254, -0.7031500339508057, -67.80615997314453], + [0.016124891117215157, 0.7030209898948669, 1.8722984790802002, -76.60822296142578], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From fd98f2a6b01aecf65d2a194f16fc65d71897b220 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:47:07 -0400 Subject: [PATCH 249/463] fix complex event files --- ...g_events.tsv => sub-06_ses-002_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-06_ses-002_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-06_ses-002_task-mario3_run-03_events.tsv} | 0 .../func/sub-06_ses-002_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-06_ses-002_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-06_ses-002_task-mario3_run-04_events.tsv} | 0 .../func/sub-06_ses-002_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-06_ses-002_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-06/ses-002/func/{sub-06_ses-002_task-mario3_run-01_part-mag_events.tsv => sub-06_ses-002_task-mario3_run-01_events.tsv} (100%) rename sub-06/ses-002/func/{sub-06_ses-002_task-mario3_run-01_part-phase_events.tsv => sub-06_ses-002_task-mario3_run-02_events.tsv} (100%) rename sub-06/ses-002/func/{sub-06_ses-002_task-mario3_run-02_part-mag_events.tsv => sub-06_ses-002_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_part-phase_events.tsv rename sub-06/ses-002/func/{sub-06_ses-002_task-mario3_run-02_part-phase_events.tsv => sub-06_ses-002_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-01_part-mag_events.tsv b/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-01_events.tsv similarity index 100% rename from sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-01_part-mag_events.tsv rename to sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-01_events.tsv diff --git a/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-01_part-phase_events.tsv b/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-02_events.tsv similarity index 100% rename from sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-01_part-phase_events.tsv rename to sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-02_events.tsv diff --git a/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-02_part-mag_events.tsv b/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_events.tsv similarity index 100% rename from sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-02_part-mag_events.tsv rename to sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_events.tsv diff --git a/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_part-mag_events.tsv b/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_part-phase_events.tsv b/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-02_part-phase_events.tsv b/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_events.tsv similarity index 100% rename from sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-02_part-phase_events.tsv rename to sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_events.tsv diff --git a/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_part-mag_events.tsv b/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_part-phase_events.tsv b/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-002/func/sub-06_ses-002_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 6726ae267f222a3e14da788cc6be4feaaf9c1a90 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:47:14 -0400 Subject: [PATCH 250/463] fix fmap phase --- ...3_ses-005_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-005_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-005_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-005_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-005_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-005_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-005_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-005_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - sub-03/ses-005/sub-03_ses-005_scans.tsv | 2 +- 29 files changed, 1 insertion(+), 1097 deletions(-) rename sub-03/ses-005/fmap/{sub-03_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-005_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-005/fmap/{sub-03_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-005_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-005/fmap/{sub-03_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-005_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-005/fmap/{sub-03_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-005_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-005/fmap/{sub-03_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-005_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-005/fmap/{sub-03_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-005_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-005/fmap/{sub-03_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-005_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-005/fmap/{sub-03_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-005_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-03/ses-005/fmap/{sub-03_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-03_ses-005_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-03/ses-005/fmap/{sub-03_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-03_ses-005_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-03/ses-005/fmap/{sub-03_ses-005_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-03_ses-005_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-03/ses-005/fmap/{sub-03_ses-005_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-03_ses-005_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-03/ses-005/fmap/{sub-03_ses-005_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-03_ses-005_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-03/ses-005/fmap/{sub-03_ses-005_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-03_ses-005_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 5bd9a1531..000000000 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:04:39.130000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999821, 0.00162199, 0.0188542, 0.00401353, 0.955479, -0.295032], - "ImageOrientationText": "Tra>Cor(-17.2)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - 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b/sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 91dc4cd82..000000000 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/6j/6Z/MD5E-s3334586--83d21a479d35c2e075c2bb7ca491b02a.nii.gz/MD5E-s3334586--83d21a479d35c2e075c2bb7ca491b02a.nii.gz \ No newline at end of file diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 65c224ce9..000000000 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:04:28.700000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 232.555, - "WipMemBlock": "40650484-dbed-4c55-8964-cdbe99990940||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index bed398db6..000000000 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/PK/52/MD5E-s1112200--cf64eb9924f9156fda8826f9d538f0fc.nii.gz/MD5E-s1112200--cf64eb9924f9156fda8826f9d538f0fc.nii.gz \ No newline at end of file diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 3169bfc3c..000000000 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:06:25.870000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 232.555, - "WipMemBlock": "b13a0602-b6aa-4383-b199-1c4f8bfb3e5f||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index f43d77fd3..000000000 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Gw/w3/MD5E-s1103605--61a405373b160fc9cdd7e75ebc1c5c22.nii.gz/MD5E-s1103605--61a405373b160fc9cdd7e75ebc1c5c22.nii.gz \ No newline at end of file diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index d5c8101a9..000000000 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:21:52.560000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999821, - 0.00162199, - 0.0188542, - 0.00401353, - 0.955479, - -0.295032 - ], - "ImageOrientationText": "Tra>Cor(-17.2)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.054717, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 626, - -7222, - -8756, - 680, - 80, - 14, - 39, - -6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 232.555, - "WipMemBlock": "5e2cce85-f616-4b8d-a217-1af57f211571||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 86c7ee4fa..000000000 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/2V/V4/MD5E-s1103649--1b512c981a0d6b7deed044b6e8615926.nii.gz/MD5E-s1103649--1b512c981a0d6b7deed044b6e8615926.nii.gz \ No newline at end of file diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 5d2896c87..000000000 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:30:54.007500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999821, - 0.00162199, - 0.0188542, - 0.00401353, - 0.955479, - -0.295032 - ], - "ImageOrientationText": "Tra>Cor(-17.2)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.054717, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 626, - -7222, - -8756, - 680, - 80, - 14, - 39, - -6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 232.555, - "WipMemBlock": "1fe710d6-ed96-4bf5-8e17-77850141ccc5||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 54cdebd7c..000000000 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/63/68/MD5E-s1103684--94653260a00e3b6de5059fe3014ef8eb.nii.gz/MD5E-s1103684--94653260a00e3b6de5059fe3014ef8eb.nii.gz \ No newline at end of file diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 4ebe3cce7..000000000 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:40:29.947500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999821, - 0.00162199, - 0.0188542, - 0.00401353, - 0.955479, - -0.295032 - ], - "ImageOrientationText": "Tra>Cor(-17.2)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.054717, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 626, - -7222, - -8756, - 680, - 80, - 14, - 39, - -6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 232.555, - "WipMemBlock": "b936a334-bd5d-4d09-a270-3a0ac5c2610f||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 181ea1bbc..000000000 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/f1/9F/MD5E-s1103692--4fcf3b8ed0551c5bbe1cd6f603192f35.nii.gz/MD5E-s1103692--4fcf3b8ed0551c5bbe1cd6f603192f35.nii.gz \ No newline at end of file diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index 17182f2b9..000000000 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:43:2.562500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999821, - 0.00162199, - 0.0188542, - 0.00401353, - 0.955479, - -0.295032 - ], - "ImageOrientationText": "Tra>Cor(-17.2)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.054717, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 626, - -7222, - -8756, - 680, - 80, - 14, - 39, - -6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 232.555, - "WipMemBlock": "ebfe47a6-e012-477b-b92e-5ed3ba52cdc8||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index 1ad85e21f..000000000 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/kJ/Kp/MD5E-s1103704--c1394f5a4b33b472da5061412b1622b1.nii.gz/MD5E-s1103704--c1394f5a4b33b472da5061412b1622b1.nii.gz \ No newline at end of file diff --git a/sub-03/ses-005/sub-03_ses-005_scans.tsv b/sub-03/ses-005/sub-03_ses-005_scans.tsv index 616838a54..7894afeb9 120000 --- a/sub-03/ses-005/sub-03_ses-005_scans.tsv +++ b/sub-03/ses-005/sub-03_ses-005_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/54/mW/MD5E-s3943--eaf3496f247755364dff8207ec48a62f.tsv/MD5E-s3943--eaf3496f247755364dff8207ec48a62f.tsv \ No newline at end of file +../../.git/annex/objects/31/kV/MD5E-s3100--95fd272ee17e536d75d31523b88a92c1.tsv/MD5E-s3100--95fd272ee17e536d75d31523b88a92c1.tsv \ No newline at end of file From e24e0fc9ac596f33f3e7af349acd48538ce38621 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:47:22 -0400 Subject: [PATCH 251/463] fix fmap phase --- ...2_ses-016_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-016_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-016_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-016_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-016_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-016_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-016_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-016_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - sub-02/ses-016/sub-02_ses-016_scans.tsv | 2 +- 29 files changed, 1 insertion(+), 1097 deletions(-) rename sub-02/ses-016/fmap/{sub-02_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-016_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-016/fmap/{sub-02_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-016_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-016/fmap/{sub-02_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-016_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-016/fmap/{sub-02_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-016_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-016/fmap/{sub-02_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-016_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-016/fmap/{sub-02_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-016_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-016/fmap/{sub-02_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-016_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-016/fmap/{sub-02_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-016_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-016/fmap/{sub-02_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-016_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-016/fmap/{sub-02_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-016_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-02/ses-016/fmap/{sub-02_ses-016_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-02_ses-016_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-02/ses-016/fmap/{sub-02_ses-016_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-02_ses-016_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-02/ses-016/fmap/{sub-02_ses-016_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-02_ses-016_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-02/ses-016/fmap/{sub-02_ses-016_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-02_ses-016_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index fce0ce738..000000000 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:11:46.362500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.998303, 0.0150197, 0.0562623, 0.0149855, 0.867364, -0.497449], - "ImageOrientationText": "Tra>Cor(-29.9)>Sag(3.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0560901, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [619, 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0.9948974251747131, 1.7313339710235596, -98.86970520019531], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99830303888915, 0.01501970319936, 0.05626234140598, 0.01498550947068, 0.86736395050446, -0.4974487027536], - "ImagePositionPatient": [-844.04484051493, -771.84478755858, 324.78839663533], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.260219, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "143058.604000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.05609005519698, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "151232.867000", - "SliceLocation": -55.298164441952, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000250943, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "143058.522000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["151146.362500", "151147.852500", "151149.342500"], - "ContentTime": ["151232.869000", "151232.872000", "151232.874000"], - "InstanceCreationTime": ["151232.869000", "151232.872000", "151232.874000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4820.0, 4818.0, 4812.0], - "WindowWidth": [18670.0, 18672.0, 18662.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index f3274e426..000000000 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/91/0V/MD5E-s3333143--d055cafd9c1e27e18847245d4c60dc89.nii.gz/MD5E-s3333143--d055cafd9c1e27e18847245d4c60dc89.nii.gz \ No newline at end of file diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 2419a89fc..000000000 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:11:35.932500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998303, - 0.0150197, - 0.0562623, - 0.0149855, - 0.867364, - -0.497449 - ], - "ImageOrientationText": "Tra>Cor(-29.9)>Sag(3.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0560901, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 619, - -7183, - -8858, - 290, - 25, - -156, - -61, - 31 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 301.694, - "WipMemBlock": "3aaecfaf-db96-4ba6-bac5-992227fa9d3f||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index ae9d8e67c..000000000 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/9G/Xj/MD5E-s1112273--4b95a9a05a70cfc34520a67eef4b1fd8.nii.gz/MD5E-s1112273--4b95a9a05a70cfc34520a67eef4b1fd8.nii.gz \ No newline at end of file diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index aa2b4f320..000000000 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:19:45.220000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998303, - 0.0150197, - 0.0562623, - 0.0149855, - 0.867364, - -0.497449 - ], - "ImageOrientationText": "Tra>Cor(-29.9)>Sag(3.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.070332, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 619, - -7183, - -8858, - 290, - 25, - -156, - -61, - 31 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 301.694, - "WipMemBlock": "89bbb75d-8f7d-4675-a92d-bee56e0cbf6b||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index e02ca46f0..000000000 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/MV/84/MD5E-s1103362--b01ff5cfd5f2a46a1965180972c16747.nii.gz/MD5E-s1103362--b01ff5cfd5f2a46a1965180972c16747.nii.gz \ No newline at end of file diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 6d518e2bd..000000000 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:29:50.700000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998303, - 0.0150197, - 0.0562623, - 0.0149855, - 0.867364, - -0.497449 - ], - "ImageOrientationText": "Tra>Cor(-29.9)>Sag(3.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.070332, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 619, - -7183, - -8858, - 290, - 25, - -156, - -61, - 31 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 301.694, - "WipMemBlock": "5a023ff6-e3b2-4c1d-a8e6-6121dcafe0d6||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 5b242a675..000000000 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/v7/JX/MD5E-s1103114--74d72eb42726dd3128f099571e805f72.nii.gz/MD5E-s1103114--74d72eb42726dd3128f099571e805f72.nii.gz \ No newline at end of file diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 7b2cc35a0..000000000 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:39:11.587500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998303, - 0.0150197, - 0.0562623, - 0.0149855, - 0.867364, - -0.497449 - ], - "ImageOrientationText": "Tra>Cor(-29.9)>Sag(3.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.070332, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 619, - -7183, - -8858, - 290, - 25, - -156, - -61, - 31 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 301.694, - "WipMemBlock": "af9674ee-d4f0-4d1e-945b-78618abbe691||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 9037cf421..000000000 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Pz/Wf/MD5E-s1103376--ac1b505394d4074595832ac030f07541.nii.gz/MD5E-s1103376--ac1b505394d4074595832ac030f07541.nii.gz \ No newline at end of file diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index b472df274..000000000 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:51:49.012500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998303, - 0.0150197, - 0.0562623, - 0.0149855, - 0.867364, - -0.497449 - ], - "ImageOrientationText": "Tra>Cor(-29.9)>Sag(3.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.070332, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 619, - -7183, - -8858, - 290, - 25, - -156, - -61, - 31 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 301.694, - "WipMemBlock": "f14b199c-e2c8-4b86-918e-17be75c73cce||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 53392b5ec..000000000 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3F/Z5/MD5E-s1103387--cce16106e74fad1dd71162671da3a1eb.nii.gz/MD5E-s1103387--cce16106e74fad1dd71162671da3a1eb.nii.gz \ No newline at end of file diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index fc04fe70d..000000000 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:02:52.380000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998303, - 0.0150197, - 0.0562623, - 0.0149855, - 0.867364, - -0.497449 - ], - "ImageOrientationText": "Tra>Cor(-29.9)>Sag(3.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-05", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.070332, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 619, - -7183, - -8858, - 290, - 25, - -156, - -61, - 31 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 301.694, - "WipMemBlock": "11aaeb0c-4633-436c-ae39-4b730435c44e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index 4dda16e2e..000000000 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/fv/m3/MD5E-s1103488--9942870c723685f499d4d3000a5d56a2.nii.gz/MD5E-s1103488--9942870c723685f499d4d3000a5d56a2.nii.gz \ No newline at end of file diff --git a/sub-02/ses-016/sub-02_ses-016_scans.tsv b/sub-02/ses-016/sub-02_ses-016_scans.tsv index e6f34aa08..a062815b6 120000 --- a/sub-02/ses-016/sub-02_ses-016_scans.tsv +++ b/sub-02/ses-016/sub-02_ses-016_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/7G/w0/MD5E-s3911--0a4e76a298d2ca43735b95bbd7fdbff6.tsv/MD5E-s3911--0a4e76a298d2ca43735b95bbd7fdbff6.tsv \ No newline at end of file +../../.git/annex/objects/7V/m8/MD5E-s3068--c6269d63e728a3fe261b55df4fcbcee1.tsv/MD5E-s3068--c6269d63e728a3fe261b55df4fcbcee1.tsv \ No newline at end of file From 4d7e6dc22d69c47aa809f0b682231ba2cb990a19 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:47:25 -0400 Subject: [PATCH 252/463] fix complex event files --- ...g_events.tsv => sub-03_ses-005_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-03_ses-005_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-03_ses-005_task-mario3_run-03_events.tsv} | 0 .../func/sub-03_ses-005_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-03_ses-005_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-03_ses-005_task-mario3_run-04_events.tsv} | 0 .../func/sub-03_ses-005_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-03_ses-005_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-03/ses-005/func/{sub-03_ses-005_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-005_task-mario3_run-01_events.tsv} (100%) rename sub-03/ses-005/func/{sub-03_ses-005_task-mario3_run-01_part-phase_events.tsv => sub-03_ses-005_task-mario3_run-02_events.tsv} (100%) rename sub-03/ses-005/func/{sub-03_ses-005_task-mario3_run-02_part-mag_events.tsv => sub-03_ses-005_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_part-phase_events.tsv rename sub-03/ses-005/func/{sub-03_ses-005_task-mario3_run-02_part-phase_events.tsv => sub-03_ses-005_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-02_events.tsv similarity index 100% rename from sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-01_part-phase_events.tsv rename to sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-02_events.tsv diff --git a/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-02_part-mag_events.tsv b/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_events.tsv similarity index 100% rename from sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-02_part-mag_events.tsv rename to sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_events.tsv diff --git a/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_part-mag_events.tsv b/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_part-phase_events.tsv b/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-02_part-phase_events.tsv b/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_events.tsv similarity index 100% rename from sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-02_part-phase_events.tsv rename to sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_events.tsv diff --git a/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-mag_events.tsv b/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-phase_events.tsv b/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-005/func/sub-03_ses-005_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 0c7f242e3e60b2b899455323c450c03c292e57e3 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:47:33 -0400 Subject: [PATCH 253/463] fix complex event files --- ...g_events.tsv => sub-02_ses-016_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-02_ses-016_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-02_ses-016_task-mario3_run-03_events.tsv} | 0 .../func/sub-02_ses-016_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-02_ses-016_task-mario3_run-04_events.tsv} | 0 .../func/sub-02_ses-016_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-02_ses-016_task-mario3_run-04_part-phase_events.tsv | 1 - ...g_events.tsv => sub-02_ses-016_task-mario3_run-05_events.tsv} | 0 .../func/sub-02_ses-016_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-02_ses-016_task-mario3_run-05_part-phase_events.tsv | 1 - 10 files changed, 5 deletions(-) rename sub-02/ses-016/func/{sub-02_ses-016_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-016_task-mario3_run-01_events.tsv} (100%) rename sub-02/ses-016/func/{sub-02_ses-016_task-mario3_run-01_part-phase_events.tsv => sub-02_ses-016_task-mario3_run-02_events.tsv} (100%) rename sub-02/ses-016/func/{sub-02_ses-016_task-mario3_run-02_part-mag_events.tsv => sub-02_ses-016_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-03_part-phase_events.tsv rename sub-02/ses-016/func/{sub-02_ses-016_task-mario3_run-02_part-phase_events.tsv => sub-02_ses-016_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_part-phase_events.tsv rename sub-02/ses-016/func/{sub-02_ses-016_task-mario3_run-03_part-mag_events.tsv => sub-02_ses-016_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_part-phase_events.tsv diff --git a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_events.tsv similarity index 100% rename from sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_part-phase_events.tsv rename to sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_events.tsv diff --git a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_part-mag_events.tsv b/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-03_events.tsv similarity index 100% rename from sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_part-mag_events.tsv rename to sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-03_events.tsv diff --git a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_part-phase_events.tsv b/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_events.tsv similarity index 100% rename from sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_part-phase_events.tsv rename to sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_events.tsv diff --git a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_part-mag_events.tsv b/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_part-phase_events.tsv b/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-03_part-mag_events.tsv b/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_events.tsv similarity index 100% rename from sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-03_part-mag_events.tsv rename to sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_events.tsv diff --git a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_part-mag_events.tsv b/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_part-phase_events.tsv b/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From bdb16bbf2c07cb7229dd65a8e888f1acd70e311b Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:47:46 -0400 Subject: [PATCH 254/463] fix fmap phase --- ...6_ses-004_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-004_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-004_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-004_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-004_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-004_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-06/ses-004/sub-06_ses-004_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-06/ses-004/fmap/{sub-06_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-06_ses-004_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-004/fmap/{sub-06_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-004_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-004/fmap/{sub-06_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-06_ses-004_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-004/fmap/{sub-06_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-004_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-004/fmap/{sub-06_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-06_ses-004_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-06/ses-004/fmap/{sub-06_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-06_ses-004_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-06/ses-004/fmap/{sub-06_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-06_ses-004_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-06/ses-004/fmap/{sub-06_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-06_ses-004_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-06/ses-004/fmap/{sub-06_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-06_ses-004_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-06/ses-004/fmap/{sub-06_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-06_ses-004_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 58d555198..000000000 --- a/sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:57:10.002500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999387, -0.0340653, 0.00806245, 0.0347248, 0.93554, -0.35151], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - 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"dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.999387088476, -0.0340652954809, 0.008062445737, 0.03472475437853, 0.93553971512281, -0.3515105017795], - "ImagePositionPatient": [-862.4959300021, -781.18839545624, 245.83312176921], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.259023, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "155521.385000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.03376765599232, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "155756.983000", - "SliceLocation": -48.332054829285, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000295413, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "155521.322000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["155710.002500", "155711.492500", "155712.982500"], - "ContentTime": ["155756.985000", "155756.988000", "155756.990000"], - "InstanceCreationTime": ["155756.985000", "155756.988000", "155756.990000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4812.0, 4812.0, 4788.0], - "WindowWidth": [18518.0, 18516.0, 18496.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 23a00a543..000000000 --- a/sub-06/ses-004/fmap/sub-06_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/KV/Qm/MD5E-s3334761--2427e102c1a2156bfade5e1450011957.nii.gz/MD5E-s3334761--2427e102c1a2156bfade5e1450011957.nii.gz \ No newline at end of file diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index ebf62e2ba..000000000 --- a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:56:59.572500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999387, - -0.0340653, - 0.00806245, - 0.0347248, - 0.93554, - -0.35151 - ], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0337677, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 627, - -7249, - -8858, - 543, - 12, - -233, - -59, - -18 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 232.326, - "WipMemBlock": "3bbb577d-9094-4eef-9616-e6f20c12f3bf||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index eb734ada4..000000000 --- a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/qk/QW/MD5E-s1112188--79adbcc8da5afb7eb5dd540f6796b3ac.nii.gz/MD5E-s1112188--79adbcc8da5afb7eb5dd540f6796b3ac.nii.gz \ No newline at end of file diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index c24729f4c..000000000 --- a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:58:20.085000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999387, - -0.0340653, - 0.00806245, - 0.0347248, - 0.93554, - -0.35151 - ], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0423417, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 627, - -7249, - -8858, - 543, - 12, - -233, - -59, - -18 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 232.326, - "WipMemBlock": "b19cec0d-6db1-4b70-aa5d-a37db923e438||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 5cdd783c2..000000000 --- a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/vM/47/MD5E-s1103409--a8e63ff5781b5e179eca36e2491ad5f1.nii.gz/MD5E-s1103409--a8e63ff5781b5e179eca36e2491ad5f1.nii.gz \ No newline at end of file diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 2b5878ff7..000000000 --- a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:07:49.565000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999387, - -0.0340653, - 0.00806245, - 0.0347248, - 0.93554, - -0.35151 - ], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0423417, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 627, - -7249, - -8858, - 543, - 12, - -233, - -59, - -18 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 232.326, - "WipMemBlock": "17fe50a4-f18a-4967-8921-478747a39e08||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 77ab9d5bd..000000000 --- a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/mK/61/MD5E-s1103510--4d1c86925268e5ca671843b5a892062a.nii.gz/MD5E-s1103510--4d1c86925268e5ca671843b5a892062a.nii.gz \ No newline at end of file diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 414fe1f20..000000000 --- a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:20:14.150000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999387, - -0.0340653, - 0.00806245, - 0.0347248, - 0.93554, - -0.35151 - ], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0423417, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 627, - -7249, - -8858, - 543, - 12, - -233, - -59, - -18 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 232.326, - "WipMemBlock": "174f1cca-caf8-4e19-9339-cd0f2b8228f1||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 75746d84c..000000000 --- a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/5P/Xx/MD5E-s1103529--f06231d8fafb38dca78a39930aace024.nii.gz/MD5E-s1103529--f06231d8fafb38dca78a39930aace024.nii.gz \ No newline at end of file diff --git a/sub-06/ses-004/sub-06_ses-004_scans.tsv b/sub-06/ses-004/sub-06_ses-004_scans.tsv index f8a177d7b..b06d2f24b 120000 --- a/sub-06/ses-004/sub-06_ses-004_scans.tsv +++ b/sub-06/ses-004/sub-06_ses-004_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/VW/wm/MD5E-s2667--ca09ce94d072330eedc63788e2943808.tsv/MD5E-s2667--ca09ce94d072330eedc63788e2943808.tsv \ No newline at end of file +../../.git/annex/objects/Pz/WM/MD5E-s2066--9a02d1912c789502f1629b75b73d018a.tsv/MD5E-s2066--9a02d1912c789502f1629b75b73d018a.tsv \ No newline at end of file From 612dcb05c6c2059df626c7b09332be425096debd Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:47:59 -0400 Subject: [PATCH 255/463] fix complex event files --- ...g_events.tsv => sub-06_ses-004_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-06_ses-004_task-mario3_run-02_events.tsv} | 0 .../func/sub-06_ses-004_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-06_ses-004_task-mario3_run-03_events.tsv} | 0 .../func/sub-06_ses-004_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-06_ses-004_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-06/ses-004/func/{sub-06_ses-004_task-mario3_run-01_part-mag_events.tsv => sub-06_ses-004_task-mario3_run-01_events.tsv} (100%) rename sub-06/ses-004/func/{sub-06_ses-004_task-mario3_run-01_part-phase_events.tsv => sub-06_ses-004_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-02_part-phase_events.tsv rename sub-06/ses-004/func/{sub-06_ses-004_task-mario3_run-02_part-mag_events.tsv => sub-06_ses-004_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-01_part-mag_events.tsv b/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-01_events.tsv similarity index 100% rename from sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-01_part-mag_events.tsv rename to sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-01_events.tsv diff --git a/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-01_part-phase_events.tsv b/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-02_events.tsv similarity index 100% rename from sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-01_part-phase_events.tsv rename to sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-02_events.tsv diff --git a/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-02_part-phase_events.tsv b/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-02_part-mag_events.tsv b/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_events.tsv similarity index 100% rename from sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-02_part-mag_events.tsv rename to sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_events.tsv diff --git a/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-mag_events.tsv b/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-phase_events.tsv b/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-004/func/sub-06_ses-004_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 0133977390f9c9aef3f64c08a1538029bd81d4ab Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:49:34 -0400 Subject: [PATCH 256/463] fill IntendedFor --- ...6_ses-002_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...6_ses-002_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...6_ses-002_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...6_ses-002_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...6_ses-002_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_epi.json b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_epi.json index 00f2fcd21..fd5c8a174 100644 --- a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998782, - -0.0490697, - 0.0051772, - 0.0476255, - 0.93128, - -0.361179 - ], + "ImageOrientationPatientDICOM": [0.998782, -0.0490697, 0.0051772, 0.0476255, 0.93128, -0.361179], "ImageOrientationText": "Tra>Cor(-21.2)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-06_ses-002_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-002/func/sub-06_ses-002_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-002/func/sub-06_ses-002_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-002/func/sub-06_ses-002_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 623, - -7253, - -8836, - 529, - -3, - -226, - -107, - -9 - ], + "ShimSetting": [623, -7253, -8836, 529, -3, -226, -107, -9], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_epi.json b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_epi.json index 10d2e5bbf..988355465 100644 --- a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998782, - -0.0490697, - 0.0051772, - 0.0476255, - 0.93128, - -0.361179 - ], + "ImageOrientationPatientDICOM": [0.998782, -0.0490697, 0.0051772, 0.0476255, 0.93128, -0.361179], "ImageOrientationText": "Tra>Cor(-21.2)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-06_ses-002_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 623, - -7253, - -8836, - 529, - -3, - -226, - -107, - -9 - ], + "ShimSetting": [623, -7253, -8836, 529, -3, -226, -107, -9], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_epi.json b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_epi.json index de2dbf615..5b99e109d 100644 --- a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998782, - -0.0490697, - 0.0051772, - 0.0476255, - 0.93128, - -0.361179 - ], + "ImageOrientationPatientDICOM": [0.998782, -0.0490697, 0.0051772, 0.0476255, 0.93128, -0.361179], "ImageOrientationText": "Tra>Cor(-21.2)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-06_ses-002_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 623, - -7253, - -8836, - 529, - -3, - -226, - -107, - -9 - ], + "ShimSetting": [623, -7253, -8836, 529, -3, -226, -107, -9], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_epi.json b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_epi.json index 502c564da..cbb39ed4f 100644 --- a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998782, - -0.0490697, - 0.0051772, - 0.0476255, - 0.93128, - -0.361179 - ], + "ImageOrientationPatientDICOM": [0.998782, -0.0490697, 0.0051772, 0.0476255, 0.93128, -0.361179], "ImageOrientationText": "Tra>Cor(-21.2)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-06_ses-002_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 623, - -7253, - -8836, - 529, - -3, - -226, - -107, - -9 - ], + "ShimSetting": [623, -7253, -8836, 529, -3, -226, -107, -9], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_epi.json b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_epi.json index 89f0794c2..25104e01e 100644 --- a/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-06/ses-002/fmap/sub-06_ses-002_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998782, - -0.0490697, - 0.0051772, - 0.0476255, - 0.93128, - -0.361179 - ], + "ImageOrientationPatientDICOM": [0.998782, -0.0490697, 0.0051772, 0.0476255, 0.93128, -0.361179], "ImageOrientationText": "Tra>Cor(-21.2)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-06_ses-002_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 623, - -7253, - -8836, - 529, - -3, - -226, - -107, - -9 - ], + "ShimSetting": [623, -7253, -8836, 529, -3, -226, -107, -9], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 242645ac76bde625251e79aff2fa4544b9a2309b Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:49:43 -0400 Subject: [PATCH 257/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-03_ses-016_acq-axial_localizer.json | 81 +++ .../sub-03_ses-016_acq-axial_localizer.nii.gz | 1 + .../sub-03_ses-016_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-016_acq-coronal_localizer.nii.gz | 1 + ...sub-03_ses-016_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-016_acq-sagittal_localizer.nii.gz | 1 + sub-03/ses-016/anat/sub-03_ses-016_scout.json | 542 ++++++++++++++++++ .../ses-016/anat/sub-03_ses-016_scout.nii.gz | 1 + ...6_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-016_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...16_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...016_task-mario3_run-01_part-mag_events.tsv | 1 + ...016_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...16_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-01_part-phase_events.tsv | 1 + ...6_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-016_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...16_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...016_task-mario3_run-02_part-mag_events.tsv | 1 + ...016_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...16_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-02_part-phase_events.tsv | 1 + ...6_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-016_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...16_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...016_task-mario3_run-03_part-mag_events.tsv | 1 + ...016_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...16_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-03_part-phase_events.tsv | 1 + ...6_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-016_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...16_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...016_task-mario3_run-04_part-mag_events.tsv | 1 + ...016_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...16_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-04_part-phase_events.tsv | 1 + ...6_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-03/ses-016/sub-03_ses-016_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5409 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-016/anat/sub-03_ses-016_acq-axial_localizer.json create mode 120000 sub-03/ses-016/anat/sub-03_ses-016_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-016/anat/sub-03_ses-016_acq-coronal_localizer.json create mode 120000 sub-03/ses-016/anat/sub-03_ses-016_acq-coronal_localizer.nii.gz create mode 100644 sub-03/ses-016/anat/sub-03_ses-016_acq-sagittal_localizer.json create mode 120000 sub-03/ses-016/anat/sub-03_ses-016_acq-sagittal_localizer.nii.gz create mode 100644 sub-03/ses-016/anat/sub-03_ses-016_scout.json create mode 120000 sub-03/ses-016/anat/sub-03_ses-016_scout.nii.gz create mode 100644 sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_part-phase_sbref.nii.gz create mode 120000 sub-03/ses-016/sub-03_ses-016_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index ebb5f3bf1..226472a7c 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit ebb5f3bf13dc44b8fe83742011846965c2fbc2c0 +Subproject commit 226472a7cd79cb35f6afb9185cc788fb3f911372 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-03/ses-016/anat/sub-03_ses-016_acq-axial_localizer.json b/sub-03/ses-016/anat/sub-03_ses-016_acq-axial_localizer.json new file mode 100644 index 000000000..b027d5d92 --- /dev/null +++ b/sub-03/ses-016/anat/sub-03_ses-016_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "14:02:18.197500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0358713, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 221.793 +} \ No newline at end of file diff --git a/sub-03/ses-016/anat/sub-03_ses-016_acq-axial_localizer.nii.gz b/sub-03/ses-016/anat/sub-03_ses-016_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..26dbcc1c5 --- /dev/null +++ b/sub-03/ses-016/anat/sub-03_ses-016_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/7X/K2/MD5E-s165323--575116404c629b7425cc15d244f6ace6.nii.gz/MD5E-s165323--575116404c629b7425cc15d244f6ace6.nii.gz \ No newline at end of file diff --git a/sub-03/ses-016/anat/sub-03_ses-016_acq-coronal_localizer.json b/sub-03/ses-016/anat/sub-03_ses-016_acq-coronal_localizer.json new file mode 100644 index 000000000..6187b7e7b --- /dev/null +++ b/sub-03/ses-016/anat/sub-03_ses-016_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "14:02:25.187500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0358713, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 221.793 +} \ No newline at end of file diff --git a/sub-03/ses-016/anat/sub-03_ses-016_acq-coronal_localizer.nii.gz b/sub-03/ses-016/anat/sub-03_ses-016_acq-coronal_localizer.nii.gz new file mode 120000 index 000000000..36291fc8d --- /dev/null +++ b/sub-03/ses-016/anat/sub-03_ses-016_acq-coronal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/k7/qK/MD5E-s183270--cc7c5afe6ce48e57517a586c2d52e72c.nii.gz/MD5E-s183270--cc7c5afe6ce48e57517a586c2d52e72c.nii.gz \ No newline at end of file diff --git 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+../../.git/annex/objects/4K/Zq/MD5E-s3289--044877769fd879bc53a38ddd8f7facf5.tsv/MD5E-s3289--044877769fd879bc53a38ddd8f7facf5.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..43e0a9f7c --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999346, 0.0336459, 0.013212, -0.0291362, 0.966112, -0.256472], + "ImageOrientationText": "Tra>Cor(-14.8)>Sag(1.2)", + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0528349, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [620, -7231, -8775, 686, 67, -41, 36, -10], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 221.793, + "dcmmeta_affine": [ + [-1.9986929893493652, -0.05827244371175766, 0.04278694838285446, 110.75809478759766], + [-0.0672917291522026, 1.9322246313095093, -0.5118394494056702, -70.68160247802734], + [0.026423929259181023, 0.5129445791244507, 1.9329224824905396, -58.12141418457031], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 7f85c7e05ddb9c05afbca3d5f7e97a890f3fe4ed Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:50:43 -0400 Subject: [PATCH 258/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..7b328ac62 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = e007ea67-ba7d-4447-885d-261d81610979 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..48845d1e6 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 48845d1e64516d54a575e765a88957ee50b09041 From 14b1df1d431ca03bfb54391c89dfed900ec444b6 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:50:52 -0400 Subject: [PATCH 259/463] fill IntendedFor --- ...3_ses-005_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...3_ses-005_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...3_ses-005_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...3_ses-005_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...3_ses-005_acq-sbref_dir-PA_run-05_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_epi.json index 81b27dd4c..303c5e64a 100644 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999821, - 0.00162199, - 0.0188542, - 0.00401353, - 0.955479, - -0.295032 - ], + "ImageOrientationPatientDICOM": [0.999821, 0.00162199, 0.0188542, 0.00401353, 0.955479, -0.295032], "ImageOrientationText": "Tra>Cor(-17.2)>Sag(1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-03_ses-005_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-005/func/sub-03_ses-005_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-005/func/sub-03_ses-005_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-005/func/sub-03_ses-005_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 626, - -7222, - -8756, - 680, - 80, - 14, - 39, - -6 - ], + "ShimSetting": [626, -7222, -8756, 680, 80, 14, 39, -6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_epi.json index 43ae35c28..542f31d78 100644 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999821, - 0.00162199, - 0.0188542, - 0.00401353, - 0.955479, - -0.295032 - ], + "ImageOrientationPatientDICOM": [0.999821, 0.00162199, 0.0188542, 0.00401353, 0.955479, -0.295032], "ImageOrientationText": "Tra>Cor(-17.2)>Sag(1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-03_ses-005_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 626, - -7222, - -8756, - 680, - 80, - 14, - 39, - -6 - ], + "ShimSetting": [626, -7222, -8756, 680, 80, 14, 39, -6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_epi.json index 99025dbf5..07c18c258 100644 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999821, - 0.00162199, - 0.0188542, - 0.00401353, - 0.955479, - -0.295032 - ], + "ImageOrientationPatientDICOM": [0.999821, 0.00162199, 0.0188542, 0.00401353, 0.955479, -0.295032], "ImageOrientationText": "Tra>Cor(-17.2)>Sag(1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-03_ses-005_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 626, - -7222, - -8756, - 680, - 80, - 14, - 39, - -6 - ], + "ShimSetting": [626, -7222, -8756, 680, 80, 14, 39, -6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_epi.json index 4437fcd32..a27e9b1a7 100644 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999821, - 0.00162199, - 0.0188542, - 0.00401353, - 0.955479, - -0.295032 - ], + "ImageOrientationPatientDICOM": [0.999821, 0.00162199, 0.0188542, 0.00401353, 0.955479, -0.295032], "ImageOrientationText": "Tra>Cor(-17.2)>Sag(1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-03_ses-005_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 626, - -7222, - -8756, - 680, - 80, - 14, - 39, - -6 - ], + "ShimSetting": [626, -7222, -8756, 680, 80, 14, 39, -6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_epi.json b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_epi.json index 661ec0493..55031cbc4 100644 --- a/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-03/ses-005/fmap/sub-03_ses-005_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999821, - 0.00162199, - 0.0188542, - 0.00401353, - 0.955479, - -0.295032 - ], + "ImageOrientationPatientDICOM": [0.999821, 0.00162199, 0.0188542, 0.00401353, 0.955479, -0.295032], "ImageOrientationText": "Tra>Cor(-17.2)>Sag(1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-03_ses-005_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 626, - -7222, - -8756, - 680, - 80, - 14, - 39, - -6 - ], + "ShimSetting": [626, -7222, -8756, 680, 80, 14, 39, -6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 46d742c1afccd2f6eb8934072e5a4f5d88ece94a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:50:54 -0400 Subject: [PATCH 260/463] fix fmap phase --- ...3_ses-016_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-016_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-016_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-016_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-016_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-016_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-016_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-03/ses-016/sub-03_ses-016_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-03/ses-016/fmap/{sub-03_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-016_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-016/fmap/{sub-03_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-016_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-016/fmap/{sub-03_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-016_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-016/fmap/{sub-03_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-016_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-016/fmap/{sub-03_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-016_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-016/fmap/{sub-03_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-016_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-016/fmap/{sub-03_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-016_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-016/fmap/{sub-03_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-016_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-03/ses-016/fmap/{sub-03_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-03_ses-016_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-03/ses-016/fmap/{sub-03_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-03_ses-016_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-03/ses-016/fmap/{sub-03_ses-016_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-03_ses-016_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-03/ses-016/fmap/{sub-03_ses-016_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-03_ses-016_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 50cebf2dc..000000000 --- a/sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:03:37.280000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999346, 0.0336459, 0.013212, -0.0291362, 0.966112, -0.256472], - "ImageOrientationText": "Tra>Cor(-14.8)>Sag(1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.042136, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [620, -7231, -8775, 686, 67, -41, 36, -10], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 221.793, - "WipMemBlock": "9c519316-2982-4fb6-9689-74eac7f5edcb||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9986929893493652, -0.05827244371175766, 0.04278694838285446, 110.75809478759766], - [-0.0672917291522026, 1.9322246313095093, -0.5118394494056702, -70.68160247802734], - [0.026423929259181023, 0.5129445791244507, 1.9329224824905396, -58.12141418457031], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99934648635662, 0.03364586431669, 0.01321196507185, -0.0291362227678, 0.96611233832737, -0.2564722796999], - "ImagePositionPatient": [-811.06910557516, -856.16151075709, 171.80538351306], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.260223, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "135934.265000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.0421360034411, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "140423.502000", - "SliceLocation": -35.71378083697, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999509428, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "135934.194000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["140337.280000", "140338.770000", "140340.260000"], - "ContentTime": ["140423.504000", "140423.507000", "140423.510000"], - "InstanceCreationTime": ["140423.504000", "140423.507000", "140423.510000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4912.0, 4914.0, 4908.0], - "WindowWidth": [18702.0, 18698.0, 18700.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 06cbbbb59..000000000 --- a/sub-03/ses-016/fmap/sub-03_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/jz/QF/MD5E-s3334715--b28f0cf4d95deac2ece136890918d597.nii.gz/MD5E-s3334715--b28f0cf4d95deac2ece136890918d597.nii.gz \ No newline at end of file diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index d927eb41a..000000000 --- a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:03:26.850000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999346, - 0.0336459, - 0.013212, - -0.0291362, - 0.966112, - -0.256472 - ], - "ImageOrientationText": "Tra>Cor(-14.8)>Sag(1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 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a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index b245c3df3..000000000 --- a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/gK/x2/MD5E-s1112342--549772060062d4e0ba7a0d2c82e4c204.nii.gz/MD5E-s1112342--549772060062d4e0ba7a0d2c82e4c204.nii.gz \ No newline at end of file diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index c2f6dd670..000000000 --- a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:04:34.317500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999346, - 0.0336459, - 0.013212, - -0.0291362, - 0.966112, - -0.256472 - ], - "ImageOrientationText": "Tra>Cor(-14.8)>Sag(1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - 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1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 221.793, - "WipMemBlock": "70a674a3-1cdf-46ad-a8e2-8fedbf015dcd||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 68afc3b2f..000000000 --- a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Vf/mQ/MD5E-s1103630--1836a591c30629a9a84a9b07c0f8d3c5.nii.gz/MD5E-s1103630--1836a591c30629a9a84a9b07c0f8d3c5.nii.gz \ No newline at end of file diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index a0b8cc5b2..000000000 --- a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:13:20.347500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999346, - 0.0336459, - 0.013212, - -0.0291362, - 0.966112, - -0.256472 - ], - "ImageOrientationText": "Tra>Cor(-14.8)>Sag(1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0528349, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 620, - -7231, - -8775, - 686, - 67, - -41, - 36, - -10 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 221.793, - "WipMemBlock": "d5525951-9d73-4b39-a50f-2f6dcfa75617||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 11d205b7a..000000000 --- a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/K2/wJ/MD5E-s1103678--ef5c231890620c3d0bcd09cc9a33e7d2.nii.gz/MD5E-s1103678--ef5c231890620c3d0bcd09cc9a33e7d2.nii.gz \ No newline at end of file diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index f2691f7bf..000000000 --- a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:24:14.567500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999346, - 0.0336459, - 0.013212, - -0.0291362, - 0.966112, - -0.256472 - ], - "ImageOrientationText": "Tra>Cor(-14.8)>Sag(1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0528349, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 620, - -7231, - -8775, - 686, - 67, - -41, - 36, - -10 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 221.793, - "WipMemBlock": "d71b2b36-acf9-43ec-9019-1dd3a7ed53c4||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 128c50082..000000000 --- a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/q4/k4/MD5E-s1103596--230082f66f415586d95e4d0279c3d54d.nii.gz/MD5E-s1103596--230082f66f415586d95e4d0279c3d54d.nii.gz \ No newline at end of file diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 763d121c0..000000000 --- a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:32:47.465000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999346, - 0.0336459, - 0.013212, - -0.0291362, - 0.966112, - -0.256472 - ], - "ImageOrientationText": "Tra>Cor(-14.8)>Sag(1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0528349, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 620, - -7231, - -8775, - 686, - 67, - -41, - 36, - -10 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 221.793, - "WipMemBlock": "e6d61496-02b6-4941-b529-3c1334a63724||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 2e46fe216..000000000 --- a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/V7/2W/MD5E-s1103776--d80bdfb6918b700a31d755b5b944f8df.nii.gz/MD5E-s1103776--d80bdfb6918b700a31d755b5b944f8df.nii.gz \ No newline at end of file diff --git a/sub-03/ses-016/sub-03_ses-016_scans.tsv b/sub-03/ses-016/sub-03_ses-016_scans.tsv index e60ef3f6e..404854a10 120000 --- a/sub-03/ses-016/sub-03_ses-016_scans.tsv +++ b/sub-03/ses-016/sub-03_ses-016_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/4K/Zq/MD5E-s3289--044877769fd879bc53a38ddd8f7facf5.tsv/MD5E-s3289--044877769fd879bc53a38ddd8f7facf5.tsv \ No newline at end of file +../../.git/annex/objects/MX/Q7/MD5E-s2567--ec58326d4e2ca2ec85708ca289209cd0.tsv/MD5E-s2567--ec58326d4e2ca2ec85708ca289209cd0.tsv \ No newline at end of file From d5a5377a28c7b04eac4c61944152ff0406187d76 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:51:01 -0400 Subject: [PATCH 261/463] fill IntendedFor --- ...6_ses-004_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...6_ses-004_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...6_ses-004_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...6_ses-004_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_epi.json b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_epi.json index ee6123930..aafcf9a59 100644 --- a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999387, - -0.0340653, - 0.00806245, - 0.0347248, - 0.93554, - -0.35151 - ], + "ImageOrientationPatientDICOM": [0.999387, -0.0340653, 0.00806245, 0.0347248, 0.93554, -0.35151], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-06_ses-004_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-004/func/sub-06_ses-004_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-004/func/sub-06_ses-004_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 627, - -7249, - -8858, - 543, - 12, - -233, - -59, - -18 - ], + "ShimSetting": [627, -7249, -8858, 543, 12, -233, -59, -18], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_epi.json b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_epi.json index 45436ada3..35a65d0b5 100644 --- a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999387, - -0.0340653, - 0.00806245, - 0.0347248, - 0.93554, - -0.35151 - ], + "ImageOrientationPatientDICOM": [0.999387, -0.0340653, 0.00806245, 0.0347248, 0.93554, -0.35151], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-06_ses-004_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 627, - -7249, - -8858, - 543, - 12, - -233, - -59, - -18 - ], + "ShimSetting": [627, -7249, -8858, 543, 12, -233, -59, -18], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_epi.json b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_epi.json index b53c3de2e..6dd4248ca 100644 --- a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999387, - -0.0340653, - 0.00806245, - 0.0347248, - 0.93554, - -0.35151 - ], + "ImageOrientationPatientDICOM": [0.999387, -0.0340653, 0.00806245, 0.0347248, 0.93554, -0.35151], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-06_ses-004_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 627, - -7249, - -8858, - 543, - 12, - -233, - -59, - -18 - ], + "ShimSetting": [627, -7249, -8858, 543, 12, -233, -59, -18], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_epi.json b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_epi.json index 90d2735c5..f1c168ea2 100644 --- a/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-06/ses-004/fmap/sub-06_ses-004_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999387, - -0.0340653, - 0.00806245, - 0.0347248, - 0.93554, - -0.35151 - ], + "ImageOrientationPatientDICOM": [0.999387, -0.0340653, 0.00806245, 0.0347248, 0.93554, -0.35151], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-06_ses-004_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 627, - -7249, - -8858, - 543, - 12, - -233, - -59, - -18 - ], + "ShimSetting": [627, -7249, -8858, 543, 12, -233, -59, -18], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 5d795647317f56dfef9442d52b59013360bcd694 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:51:02 -0400 Subject: [PATCH 262/463] fix complex event files --- ...g_events.tsv => sub-03_ses-016_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-03_ses-016_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-03_ses-016_task-mario3_run-03_events.tsv} | 0 .../func/sub-03_ses-016_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-03_ses-016_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-03_ses-016_task-mario3_run-04_events.tsv} | 0 .../func/sub-03_ses-016_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-03_ses-016_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-03/ses-016/func/{sub-03_ses-016_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-016_task-mario3_run-01_events.tsv} (100%) rename sub-03/ses-016/func/{sub-03_ses-016_task-mario3_run-01_part-phase_events.tsv => sub-03_ses-016_task-mario3_run-02_events.tsv} (100%) rename sub-03/ses-016/func/{sub-03_ses-016_task-mario3_run-02_part-mag_events.tsv => sub-03_ses-016_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_part-phase_events.tsv rename sub-03/ses-016/func/{sub-03_ses-016_task-mario3_run-02_part-phase_events.tsv => sub-03_ses-016_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_events.tsv similarity index 100% rename from sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_part-phase_events.tsv rename to sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_events.tsv diff --git a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_part-mag_events.tsv b/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_events.tsv similarity index 100% rename from sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_part-mag_events.tsv rename to sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_events.tsv diff --git a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_part-mag_events.tsv b/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_part-phase_events.tsv b/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_part-phase_events.tsv b/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_events.tsv similarity index 100% rename from sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_part-phase_events.tsv rename to sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_events.tsv diff --git a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_part-mag_events.tsv b/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_part-phase_events.tsv b/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 1e0c2e85a49c36126eaed1de5e2d1129808ad17c Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:51:05 -0400 Subject: [PATCH 263/463] fill IntendedFor --- ...2_ses-016_acq-sbref_dir-AP_run-01_epi.json | 92 +++---------------- ...2_ses-016_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...2_ses-016_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...2_ses-016_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...2_ses-016_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- ...2_ses-016_acq-sbref_dir-PA_run-05_epi.json | 88 ++---------------- 6 files changed, 46 insertions(+), 486 deletions(-) diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_epi.json index 358291f4e..c59b25187 100644 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998303, - 0.0150197, - 0.0562623, - 0.0149855, - 0.867364, - -0.497449 - ], + "ImageOrientationPatientDICOM": [0.998303, 0.0150197, 0.0562623, 0.0149855, 0.867364, -0.497449], "ImageOrientationText": "Tra>Cor(-29.9)>Sag(3.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,19 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-02_ses-016_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-016/func/sub-02_ses-016_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-016/func/sub-02_ses-016_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-016/func/sub-02_ses-016_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-016/func/sub-02_ses-016_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +67,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 619, - -7183, - -8858, - 290, - 25, - -156, - -61, - 31 - ], + "ShimSetting": [619, -7183, -8858, 290, 25, -156, -61, 31], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_epi.json index 685a2c70c..ee197be85 100644 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998303, - 0.0150197, - 0.0562623, - 0.0149855, - 0.867364, - -0.497449 - ], + "ImageOrientationPatientDICOM": [0.998303, 0.0150197, 0.0562623, 0.0149855, 0.867364, -0.497449], "ImageOrientationText": "Tra>Cor(-29.9)>Sag(3.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-02_ses-016_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 619, - -7183, - -8858, - 290, - 25, - -156, - -61, - 31 - ], + "ShimSetting": [619, -7183, -8858, 290, 25, -156, -61, 31], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_epi.json index d522d042b..f5c1aff13 100644 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998303, - 0.0150197, - 0.0562623, - 0.0149855, - 0.867364, - -0.497449 - ], + "ImageOrientationPatientDICOM": [0.998303, 0.0150197, 0.0562623, 0.0149855, 0.867364, -0.497449], "ImageOrientationText": "Tra>Cor(-29.9)>Sag(3.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-02_ses-016_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 619, - -7183, - -8858, - 290, - 25, - -156, - -61, - 31 - ], + "ShimSetting": [619, -7183, -8858, 290, 25, -156, -61, 31], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_epi.json index ca8496b60..0699ea550 100644 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998303, - 0.0150197, - 0.0562623, - 0.0149855, - 0.867364, - -0.497449 - ], + "ImageOrientationPatientDICOM": [0.998303, 0.0150197, 0.0562623, 0.0149855, 0.867364, -0.497449], "ImageOrientationText": "Tra>Cor(-29.9)>Sag(3.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-02_ses-016_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 619, - -7183, - -8858, - 290, - 25, - -156, - -61, - 31 - ], + "ShimSetting": [619, -7183, -8858, 290, 25, -156, -61, 31], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_epi.json index 7d19a07ae..41499b8c3 100644 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998303, - 0.0150197, - 0.0562623, - 0.0149855, - 0.867364, - -0.497449 - ], + "ImageOrientationPatientDICOM": [0.998303, 0.0150197, 0.0562623, 0.0149855, 0.867364, -0.497449], "ImageOrientationText": "Tra>Cor(-29.9)>Sag(3.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-02_ses-016_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 619, - -7183, - -8858, - 290, - 25, - -156, - -61, - 31 - ], + "ShimSetting": [619, -7183, -8858, 290, 25, -156, -61, 31], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_epi.json b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_epi.json index 8e73074f5..5a19fbd82 100644 --- a/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-02/ses-016/fmap/sub-02_ses-016_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998303, - 0.0150197, - 0.0562623, - 0.0149855, - 0.867364, - -0.497449 - ], + "ImageOrientationPatientDICOM": [0.998303, 0.0150197, 0.0562623, 0.0149855, 0.867364, -0.497449], "ImageOrientationText": "Tra>Cor(-29.9)>Sag(3.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-02_ses-016_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 619, - -7183, - -8858, - 290, - 25, - -156, - -61, - 31 - ], + "ShimSetting": [619, -7183, -8858, 290, 25, -156, -61, 31], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 7b7b3d64a6317d45a8c78c2d7263197c0cd3c758 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:53:36 -0400 Subject: [PATCH 264/463] fill IntendedFor --- ...3_ses-016_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...3_ses-016_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...3_ses-016_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...3_ses-016_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...3_ses-016_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_epi.json index 82e03a1d7..5e00ebd46 100644 --- a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999346, - 0.0336459, - 0.013212, - -0.0291362, - 0.966112, - -0.256472 - ], + "ImageOrientationPatientDICOM": [0.999346, 0.0336459, 0.013212, -0.0291362, 0.966112, -0.256472], "ImageOrientationText": "Tra>Cor(-14.8)>Sag(1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-03_ses-016_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-016/func/sub-03_ses-016_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-016/func/sub-03_ses-016_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-016/func/sub-03_ses-016_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 620, - -7231, - -8775, - 686, - 67, - -41, - 36, - -10 - ], + "ShimSetting": [620, -7231, -8775, 686, 67, -41, 36, -10], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_epi.json b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_epi.json index 83c1ee033..4dcf7e376 100644 --- a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999346, - 0.0336459, - 0.013212, - -0.0291362, - 0.966112, - -0.256472 - ], + "ImageOrientationPatientDICOM": [0.999346, 0.0336459, 0.013212, -0.0291362, 0.966112, -0.256472], "ImageOrientationText": "Tra>Cor(-14.8)>Sag(1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-03_ses-016_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 620, - -7231, - -8775, - 686, - 67, - -41, - 36, - -10 - ], + "ShimSetting": [620, -7231, -8775, 686, 67, -41, 36, -10], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_epi.json b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_epi.json index 83c2a92da..1005bf640 100644 --- a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999346, - 0.0336459, - 0.013212, - -0.0291362, - 0.966112, - -0.256472 - ], + "ImageOrientationPatientDICOM": [0.999346, 0.0336459, 0.013212, -0.0291362, 0.966112, -0.256472], "ImageOrientationText": "Tra>Cor(-14.8)>Sag(1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-03_ses-016_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 620, - -7231, - -8775, - 686, - 67, - -41, - 36, - -10 - ], + "ShimSetting": [620, -7231, -8775, 686, 67, -41, 36, -10], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_epi.json b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_epi.json index 6950300db..a23143322 100644 --- a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999346, - 0.0336459, - 0.013212, - -0.0291362, - 0.966112, - -0.256472 - ], + "ImageOrientationPatientDICOM": [0.999346, 0.0336459, 0.013212, -0.0291362, 0.966112, -0.256472], "ImageOrientationText": "Tra>Cor(-14.8)>Sag(1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-03_ses-016_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 620, - -7231, - -8775, - 686, - 67, - -41, - 36, - -10 - ], + "ShimSetting": [620, -7231, -8775, 686, 67, -41, 36, -10], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_epi.json b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_epi.json index ca97ff221..579e917f0 100644 --- a/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-03/ses-016/fmap/sub-03_ses-016_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999346, - 0.0336459, - 0.013212, - -0.0291362, - 0.966112, - -0.256472 - ], + "ImageOrientationPatientDICOM": [0.999346, 0.0336459, 0.013212, -0.0291362, 0.966112, -0.256472], "ImageOrientationText": "Tra>Cor(-14.8)>Sag(1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-03_ses-016_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 620, - -7231, - -8775, - 686, - 67, - -41, - 36, - -10 - ], + "ShimSetting": [620, -7231, -8775, 686, 67, -41, 36, -10], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From ae7bf381373562d648b13953831721b13d4239b2 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 16:58:27 -0400 Subject: [PATCH 265/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..2681123c0 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 3d117eb8-0137-4cfd-bea7-33cfe9807a2d diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..f189624ce --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit f189624ce791255adaab9b3e272d090b3f90620e From 859c6aa10f3a11dbbd0390f0f3e2a058dc55105e Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:01:17 -0400 Subject: [PATCH 266/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..384cc6f8b --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 015c6d7a-b9e5-4d8b-84ca-dc0acaa7e852 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..f7aa40cfe --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit f7aa40cfe29bf25e525c83a76b09351a62c9aa07 From bf8fdd73607ccd06f099273f003c485377e9b1a5 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:01:24 -0400 Subject: [PATCH 267/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-05_ses-001_acq-axial_localizer.json | 81 +++ .../sub-05_ses-001_acq-axial_localizer.nii.gz | 1 + .../sub-05_ses-001_acq-coronal_localizer.json | 81 +++ ...ub-05_ses-001_acq-coronal_localizer.nii.gz | 1 + ...sub-05_ses-001_acq-sagittal_localizer.json | 86 +++ ...b-05_ses-001_acq-sagittal_localizer.nii.gz | 1 + sub-05/ses-001/anat/sub-05_ses-001_scout.json | 542 ++++++++++++++++++ .../ses-001/anat/sub-05_ses-001_scout.nii.gz | 1 + ...1_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-001_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-01_part-mag_events.tsv | 1 + ...001_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-01_part-phase_events.tsv | 1 + ...1_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-001_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-02_part-mag_events.tsv | 1 + ...001_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-02_part-phase_events.tsv | 1 + ...1_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-001_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-03_part-mag_events.tsv | 1 + ...001_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-03_part-phase_events.tsv | 1 + ...1_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-001_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-04_part-mag_events.tsv | 1 + ...001_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-04_part-phase_events.tsv | 1 + ...1_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-05/ses-001/sub-05_ses-001_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5409 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-05/ses-001/anat/sub-05_ses-001_acq-axial_localizer.json create mode 120000 sub-05/ses-001/anat/sub-05_ses-001_acq-axial_localizer.nii.gz create mode 100644 sub-05/ses-001/anat/sub-05_ses-001_acq-coronal_localizer.json create mode 120000 sub-05/ses-001/anat/sub-05_ses-001_acq-coronal_localizer.nii.gz create mode 100644 sub-05/ses-001/anat/sub-05_ses-001_acq-sagittal_localizer.json create mode 120000 sub-05/ses-001/anat/sub-05_ses-001_acq-sagittal_localizer.nii.gz create mode 100644 sub-05/ses-001/anat/sub-05_ses-001_scout.json create mode 120000 sub-05/ses-001/anat/sub-05_ses-001_scout.nii.gz create mode 100644 sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_part-phase_sbref.nii.gz create mode 120000 sub-05/ses-001/sub-05_ses-001_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 48845d1e6..89a1ca4c8 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 48845d1e64516d54a575e765a88957ee50b09041 +Subproject commit 89a1ca4c8d7569d4035eb2273f2c2c698af54b29 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..da8d4ae9f --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-05 50 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-05/ses-001/anat/sub-05_ses-001_acq-axial_localizer.json b/sub-05/ses-001/anat/sub-05_ses-001_acq-axial_localizer.json new file mode 100644 index 000000000..2cacbbf22 --- /dev/null +++ b/sub-05/ses-001/anat/sub-05_ses-001_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "19:07:15.030000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0563845, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 321.111 +} \ No newline at end of file diff --git a/sub-05/ses-001/anat/sub-05_ses-001_acq-axial_localizer.nii.gz b/sub-05/ses-001/anat/sub-05_ses-001_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..3d1ad6fe2 --- /dev/null +++ b/sub-05/ses-001/anat/sub-05_ses-001_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/6f/14/MD5E-s180649--e6239a69cf46ff09974bd974ae8c43e5.nii.gz/MD5E-s180649--e6239a69cf46ff09974bd974ae8c43e5.nii.gz \ No newline at end of file diff --git a/sub-05/ses-001/anat/sub-05_ses-001_acq-coronal_localizer.json b/sub-05/ses-001/anat/sub-05_ses-001_acq-coronal_localizer.json new file mode 100644 index 000000000..7d74a4f3d --- /dev/null +++ b/sub-05/ses-001/anat/sub-05_ses-001_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "19:07:22.020000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": 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--git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..121bddaea --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = c7a75ebd-8607-4481-9c99-51525b8f2a55 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..f57282915 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit f57282915b5da89e3c645fc02d271264faa7cc03 From 69245a4ae7a894ed88ba74acf9edf6212057a0a8 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:01:42 -0400 Subject: [PATCH 269/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-03_ses-014_acq-axial_localizer.json | 81 +++ .../sub-03_ses-014_acq-axial_localizer.nii.gz | 1 + .../sub-03_ses-014_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-014_acq-coronal_localizer.nii.gz | 1 + ...sub-03_ses-014_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-014_acq-sagittal_localizer.nii.gz | 1 + sub-03/ses-014/anat/sub-03_ses-014_scout.json | 671 ++++++++++++++++++ .../ses-014/anat/sub-03_ses-014_scout.nii.gz | 1 + ...4_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 +++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 +++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 ++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 ++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 ++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 ++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 ++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 ++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 ++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 ++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 ++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 ++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 ++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 ++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ...-014_task-mario3_run-01_part-mag_bold.json | 172 +++++ ...14_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...014_task-mario3_run-01_part-mag_events.tsv | 1 + ...014_task-mario3_run-01_part-mag_sbref.json | 150 ++++ ...4_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...14_task-mario3_run-01_part-phase_bold.json | 178 +++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-01_part-phase_events.tsv | 1 + ...4_task-mario3_run-01_part-phase_sbref.json | 153 ++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-014_task-mario3_run-02_part-mag_bold.json | 172 +++++ ...14_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...014_task-mario3_run-02_part-mag_events.tsv | 1 + ...014_task-mario3_run-02_part-mag_sbref.json | 150 ++++ ...4_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...14_task-mario3_run-02_part-phase_bold.json | 178 +++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-02_part-phase_events.tsv | 1 + ...4_task-mario3_run-02_part-phase_sbref.json | 153 ++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-014_task-mario3_run-03_part-mag_bold.json | 172 +++++ ...14_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...014_task-mario3_run-03_part-mag_events.tsv | 1 + ...014_task-mario3_run-03_part-mag_sbref.json | 150 ++++ ...4_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...14_task-mario3_run-03_part-phase_bold.json | 178 +++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-03_part-phase_events.tsv | 1 + ...4_task-mario3_run-03_part-phase_sbref.json | 153 ++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-014_task-mario3_run-04_part-mag_bold.json | 172 +++++ ...14_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...014_task-mario3_run-04_part-mag_events.tsv | 1 + ...014_task-mario3_run-04_part-mag_sbref.json | 150 ++++ ...4_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...14_task-mario3_run-04_part-phase_bold.json | 178 +++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-04_part-phase_events.tsv | 1 + ...4_task-mario3_run-04_part-phase_sbref.json | 153 ++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-014_task-mario3_run-05_part-mag_bold.json | 172 +++++ ...14_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...014_task-mario3_run-05_part-mag_events.tsv | 1 + ...014_task-mario3_run-05_part-mag_sbref.json | 150 ++++ ...4_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...14_task-mario3_run-05_part-phase_bold.json | 178 +++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-05_part-phase_events.tsv | 1 + ...4_task-mario3_run-05_part-phase_sbref.json | 153 ++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + sub-03/ses-014/sub-03_ses-014_scans.tsv | 1 + task-mario3_bold.json | 75 ++ 93 files changed, 6500 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-014/anat/sub-03_ses-014_acq-axial_localizer.json create mode 120000 sub-03/ses-014/anat/sub-03_ses-014_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-014/anat/sub-03_ses-014_acq-coronal_localizer.json create mode 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sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_part-mag_epi.json create mode 120000 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz create mode 100644 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sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-05_part-phase_sbref.json create mode 120000 sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-05_part-phase_sbref.nii.gz create mode 120000 sub-03/ses-014/sub-03_ses-014_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 8168e7575..e0c7f638d 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 8168e7575894101551c619a485e4149f99d8ad57 +Subproject commit e0c7f638db1ded5de93c8d03f7beb80389dd056d diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-03/ses-014/anat/sub-03_ses-014_acq-axial_localizer.json b/sub-03/ses-014/anat/sub-03_ses-014_acq-axial_localizer.json new file mode 100644 index 000000000..e45a72210 --- /dev/null +++ b/sub-03/ses-014/anat/sub-03_ses-014_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "13:42:13.202500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + 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+../../../.git/annex/objects/V6/kq/MD5E-s161245--68d1ff45ed6a7f052c2cc035fdb7e419.nii.gz/MD5E-s161245--68d1ff45ed6a7f052c2cc035fdb7e419.nii.gz \ No newline at end of file diff --git a/sub-03/ses-014/anat/sub-03_ses-014_acq-coronal_localizer.json b/sub-03/ses-014/anat/sub-03_ses-014_acq-coronal_localizer.json new file mode 100644 index 000000000..62e5a35e8 --- /dev/null +++ b/sub-03/ses-014/anat/sub-03_ses-014_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "13:42:20.192500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, 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a/sub-03/ses-014/anat/sub-03_ses-014_acq-sagittal_localizer.json b/sub-03/ses-014/anat/sub-03_ses-014_acq-sagittal_localizer.json new file mode 100644 index 000000000..5d9c3cb34 --- /dev/null +++ b/sub-03/ses-014/anat/sub-03_ses-014_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "13:42:6.212500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 0, + 1, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Sag", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.261, + 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+../../.git/annex/objects/zW/wj/MD5E-s3911--dfedf36601f9b2bf01b7f7c0a5d272d8.tsv/MD5E-s3911--dfedf36601f9b2bf01b7f7c0a5d272d8.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..2f5809615 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": 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\ No newline at end of file From 50c8fd7b18c13e241319f100865d0d4c6d814ff9 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:01:46 -0400 Subject: [PATCH 270/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-06_ses-006_acq-axial_localizer.json | 81 +++ .../sub-06_ses-006_acq-axial_localizer.nii.gz | 1 + .../sub-06_ses-006_acq-coronal_localizer.json | 81 +++ ...ub-06_ses-006_acq-coronal_localizer.nii.gz | 1 + ...sub-06_ses-006_acq-sagittal_localizer.json | 86 +++ ...b-06_ses-006_acq-sagittal_localizer.nii.gz | 1 + sub-06/ses-006/anat/sub-06_ses-006_scout.json | 542 ++++++++++++++++++ .../ses-006/anat/sub-06_ses-006_scout.nii.gz | 1 + ...6_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-006_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...06_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...006_task-mario3_run-01_part-mag_events.tsv | 1 + ...006_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-01_part-phase_events.tsv | 1 + ...6_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-006_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...06_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...006_task-mario3_run-02_part-mag_events.tsv | 1 + ...006_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-02_part-phase_events.tsv | 1 + ...6_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-006_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...06_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...006_task-mario3_run-03_part-mag_events.tsv | 1 + ...006_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-03_part-phase_events.tsv | 1 + ...6_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-06/ses-006/sub-06_ses-006_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-06/ses-006/anat/sub-06_ses-006_acq-axial_localizer.json create mode 120000 sub-06/ses-006/anat/sub-06_ses-006_acq-axial_localizer.nii.gz create mode 100644 sub-06/ses-006/anat/sub-06_ses-006_acq-coronal_localizer.json create mode 120000 sub-06/ses-006/anat/sub-06_ses-006_acq-coronal_localizer.nii.gz create mode 100644 sub-06/ses-006/anat/sub-06_ses-006_acq-sagittal_localizer.json create mode 120000 sub-06/ses-006/anat/sub-06_ses-006_acq-sagittal_localizer.nii.gz create mode 100644 sub-06/ses-006/anat/sub-06_ses-006_scout.json create mode 120000 sub-06/ses-006/anat/sub-06_ses-006_scout.nii.gz create mode 100644 sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-06/ses-006/sub-06_ses-006_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index f7aa40cfe..d054e8716 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit f7aa40cfe29bf25e525c83a76b09351a62c9aa07 +Subproject commit d054e87161693e520f0898be17a5da7c995d22d7 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..db37a3f34 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-06 41 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-06/ses-006/anat/sub-06_ses-006_acq-axial_localizer.json b/sub-06/ses-006/anat/sub-06_ses-006_acq-axial_localizer.json new file mode 100644 index 000000000..18a9633d5 --- /dev/null +++ b/sub-06/ses-006/anat/sub-06_ses-006_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:21:59.035000", + "BaseResolution": 256, + 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ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz new file mode 120000 index 000000000..890679ec6 --- /dev/null +++ b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/pj/w1/MD5E-s1103378--bb2aaefa9bd97cba39b7e35ad8c021fa.nii.gz/MD5E-s1103378--bb2aaefa9bd97cba39b7e35ad8c021fa.nii.gz \ No newline at end of file diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json new file mode 100644 index 000000000..4e66aebcd --- /dev/null +++ b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json @@ -0,0 +1,149 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + 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a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz new file mode 120000 index 000000000..1c9122699 --- /dev/null +++ b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Jf/p0/MD5E-s1099405--cc4a620272068eaab47e0bce5c13ed1b.nii.gz/MD5E-s1099405--cc4a620272068eaab47e0bce5c13ed1b.nii.gz \ No newline at end of file diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json new file mode 100644 index 000000000..a47b250fe --- /dev/null +++ b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json @@ -0,0 +1,152 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:52:13.902500", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + 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"b5309ceb-6f6e-40ff-863f-47f55cd6dfe5||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-phase_sbref.nii.gz b/sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-phase_sbref.nii.gz new file mode 120000 index 000000000..07c75d743 --- /dev/null +++ b/sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/M4/2m/MD5E-s1103413--4a62d9ea3294b68e1f873ed8def45f99.nii.gz/MD5E-s1103413--4a62d9ea3294b68e1f873ed8def45f99.nii.gz \ No newline at end of file diff --git a/sub-06/ses-006/sub-06_ses-006_scans.tsv b/sub-06/ses-006/sub-06_ses-006_scans.tsv new file mode 120000 index 000000000..dc2ef60be --- /dev/null +++ b/sub-06/ses-006/sub-06_ses-006_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/qQ/JF/MD5E-s2660--6cdcb84e2d7b3558ca37fed0f1e2983c.tsv/MD5E-s2660--6cdcb84e2d7b3558ca37fed0f1e2983c.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..f24bd5a1b --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.99817, -0.0595147, 0.0107347, 0.0598267, 0.945864, -0.319], + "ImageOrientationText": "Tra>Cor(-18.6)>Sag(-0.5)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0896126, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [624, -7265, -8834, 536, 26, -252, -53, -8], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 314.074, + "dcmmeta_affine": [ + [-1.9963394403457642, 0.11965342611074448, -0.017663218080997467, 100.93151092529297], + [0.11902938783168793, 1.8917289972305298, -0.6381170153617859, -72.47587585449219], + [0.02146943286061287, 0.6380003094673157, 1.8953876495361328, -65.78069305419922], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 04752b695821905a56b9a151a4b3a9133f9fc035 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:02:02 -0400 Subject: [PATCH 271/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-06_ses-003_acq-axial_localizer.json | 81 +++ .../sub-06_ses-003_acq-axial_localizer.nii.gz | 1 + .../sub-06_ses-003_acq-coronal_localizer.json | 81 +++ ...ub-06_ses-003_acq-coronal_localizer.nii.gz | 1 + ...sub-06_ses-003_acq-sagittal_localizer.json | 86 +++ ...b-06_ses-003_acq-sagittal_localizer.nii.gz | 1 + sub-06/ses-003/anat/sub-06_ses-003_scout.json | 542 ++++++++++++++++++ .../ses-003/anat/sub-06_ses-003_scout.nii.gz | 1 + ...3_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-003_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-01_part-mag_events.tsv | 1 + ...003_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-01_part-phase_events.tsv | 1 + ...3_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-003_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-02_part-mag_events.tsv | 1 + ...003_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-02_part-phase_events.tsv | 1 + ...3_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-003_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-03_part-mag_events.tsv | 1 + ...003_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-03_part-phase_events.tsv | 1 + ...3_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-003_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-04_part-mag_events.tsv | 1 + ...003_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-04_part-phase_events.tsv | 1 + ...3_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-06/ses-003/sub-06_ses-003_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5409 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-06/ses-003/anat/sub-06_ses-003_acq-axial_localizer.json create mode 120000 sub-06/ses-003/anat/sub-06_ses-003_acq-axial_localizer.nii.gz create mode 100644 sub-06/ses-003/anat/sub-06_ses-003_acq-coronal_localizer.json create mode 120000 sub-06/ses-003/anat/sub-06_ses-003_acq-coronal_localizer.nii.gz create mode 100644 sub-06/ses-003/anat/sub-06_ses-003_acq-sagittal_localizer.json create mode 120000 sub-06/ses-003/anat/sub-06_ses-003_acq-sagittal_localizer.nii.gz create mode 100644 sub-06/ses-003/anat/sub-06_ses-003_scout.json create mode 120000 sub-06/ses-003/anat/sub-06_ses-003_scout.nii.gz create mode 100644 sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-phase_sbref.nii.gz create mode 120000 sub-06/ses-003/sub-06_ses-003_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index f57282915..a1b6975d4 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit f57282915b5da89e3c645fc02d271264faa7cc03 +Subproject commit a1b6975d47e821617de6e23fd76fc2964f5965e6 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..db37a3f34 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-06 41 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-06/ses-003/anat/sub-06_ses-003_acq-axial_localizer.json b/sub-06/ses-003/anat/sub-06_ses-003_acq-axial_localizer.json new file mode 100644 index 000000000..8f2041811 --- /dev/null +++ b/sub-06/ses-003/anat/sub-06_ses-003_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:09:7.077500", + "BaseResolution": 256, + 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new file mode 120000 index 000000000..2df2fad11 --- /dev/null +++ b/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-phase_bold.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/fg/Q3/MD5E-s409093504--f555b56441f9bd3d2e4d9855417d575f.nii.gz/MD5E-s409093504--f555b56441f9bd3d2e4d9855417d575f.nii.gz \ No newline at end of file diff --git a/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-phase_events.tsv b/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-phase_events.tsv new file mode 120000 index 000000000..1bbdfddb5 --- /dev/null +++ b/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-phase_events.tsv @@ -0,0 +1 @@ +../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-phase_sbref.json b/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-phase_sbref.json new file mode 100644 index 000000000..108a10544 --- /dev/null +++ b/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-phase_sbref.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:39:1.065000", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTime1": 0.037, + "EchoTime2": 0.001, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Single-band reference", + "ImageOrientationPatientDICOM": [ + 0.998388, + -0.055579, + 0.0114739, + 0.056343, + 0.946541, + -0.317624 + ], + "ImageOrientationText": "Tra>Cor(-18.5)>Sag(-0.4)", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "P", + "ND", + "MOSAIC", + "PHASE" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "func_task-mario3_run-04", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + 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@@ -0,0 +1 @@ +../../.git/annex/objects/9P/Qm/MD5E-s3289--318b5277782b40d20597c59c43d69c01.tsv/MD5E-s3289--318b5277782b40d20597c59c43d69c01.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..3d5a3bb47 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + 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"HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0420194, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [629, -7278, -8798, 571, 1, -235, -32, -8], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 229.156, + "dcmmeta_affine": [ + [-1.9967767000198364, 0.11268598586320877, -0.013585363514721394, 100.61431884765625], + [0.11115794628858566, 1.8930823802947998, -0.6355177760124207, -71.58369445800781], + [0.022947870194911957, 0.6352486610412598, 1.896294355392456, -56.14326095581055], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From f18743bdc26325356423b895356676b35b080102 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:02:08 -0400 Subject: [PATCH 272/463] fix fmap phase --- ...5_ses-001_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-001_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-001_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-05/ses-001/sub-05_ses-001_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-05/ses-001/fmap/{sub-05_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-05_ses-001_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-001/fmap/{sub-05_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-001_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-001/fmap/{sub-05_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-05_ses-001_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-001/fmap/{sub-05_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-001_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-001/fmap/{sub-05_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-05_ses-001_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-05/ses-001/fmap/{sub-05_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-05_ses-001_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-05/ses-001/fmap/{sub-05_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-05_ses-001_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-05/ses-001/fmap/{sub-05_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-05_ses-001_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-05/ses-001/fmap/{sub-05_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-05_ses-001_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-05/ses-001/fmap/{sub-05_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-05_ses-001_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-05/ses-001/fmap/{sub-05_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-05_ses-001_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-05/ses-001/fmap/{sub-05_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-05_ses-001_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 312acfa26..000000000 --- a/sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:08:16.677500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999316, -0.0313383, 0.0196295, 0.036294, 0.932881, -0.358352], - "ImageOrientationText": "Tra>Cor(-21.0)>Sag(0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - 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"dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99931606384249, -0.0313382980311, 0.01962945803785, 0.03629397281602, 0.93288090907746, -0.3583517224963], - "ImagePositionPatient": [-861.53581898137, -776.25377671614, 261.74748890978], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.260178, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "190617.761000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.06623170772467, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "190903.243000", - "SliceLocation": -28.123475658949, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999702571, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "190617.684000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["190816.677500", "190818.167500", "190819.657500"], - "ContentTime": ["190903.245000", "190903.248000", "190903.250000"], - "InstanceCreationTime": ["190903.245000", "190903.248000", "190903.250000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4790.0, 4796.0, 4816.0], - "WindowWidth": [18572.0, 18554.0, 18606.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 5b2b5f9a5..000000000 --- a/sub-05/ses-001/fmap/sub-05_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/mK/5J/MD5E-s3333656--e9a9bc120df0aadd0227270b2ebe7b78.nii.gz/MD5E-s3333656--e9a9bc120df0aadd0227270b2ebe7b78.nii.gz \ No newline at end of file diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 591d1d70c..000000000 --- a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:08:6.247500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999316, - -0.0313383, - 0.0196295, - 0.036294, - 0.932881, - -0.358352 - ], - "ImageOrientationText": "Tra>Cor(-21.0)>Sag(0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0662317, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 605, - -7271, - -8809, - 436, - 29, - -353, - -24, - 33 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 321.111, - "WipMemBlock": "37262ee5-bfb8-45a4-80e6-e525a0f167b3||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 9563dfa0b..000000000 --- a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/qX/v3/MD5E-s1112234--dfe65403d6c3ec55fa702a59e9bfe439.nii.gz/MD5E-s1112234--dfe65403d6c3ec55fa702a59e9bfe439.nii.gz \ No newline at end of file diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 1cc6d2834..000000000 --- a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:09:24.510000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999316, - -0.0313383, - 0.0196295, - 0.036294, - 0.932881, - -0.358352 - ], - "ImageOrientationText": "Tra>Cor(-21.0)>Sag(0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0830488, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 605, - -7271, - -8809, - 436, - 29, - -353, - -24, - 33 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 321.111, - "WipMemBlock": "6fc7905e-7167-44ee-b436-d22815db1360||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 1fc58cce5..000000000 --- a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/z8/qv/MD5E-s1103509--88e6158ad61907b4b32bd03b4a37f6fc.nii.gz/MD5E-s1103509--88e6158ad61907b4b32bd03b4a37f6fc.nii.gz \ No newline at end of file diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 573e48a5c..000000000 --- a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:18:1.287500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999316, - -0.0313383, - 0.0196295, - 0.036294, - 0.932881, - -0.358352 - ], - "ImageOrientationText": "Tra>Cor(-21.0)>Sag(0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0830488, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 605, - -7271, - -8809, - 436, - 29, - -353, - -24, - 33 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 321.111, - "WipMemBlock": "afcf6a99-1883-4fbc-90fb-687ed12b0498||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 1fcf36a89..000000000 --- a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/pG/Ff/MD5E-s1103455--bb4183f2ecda4aa219805d9830124856.nii.gz/MD5E-s1103455--bb4183f2ecda4aa219805d9830124856.nii.gz \ No newline at end of file diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 12df0f8ea..000000000 --- a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:29:10.242500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999316, - -0.0313383, - 0.0196295, - 0.036294, - 0.932881, - -0.358352 - ], - "ImageOrientationText": "Tra>Cor(-21.0)>Sag(0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0830488, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 605, - -7271, - -8809, - 436, - 29, - -353, - -24, - 33 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 321.111, - "WipMemBlock": "5b196370-8903-44d7-9cd9-6b7ef8c60a4f||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index b4c7f33ff..000000000 --- a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/kM/vk/MD5E-s1103556--f9da7bb2e0a273cdcd91eddad394d921.nii.gz/MD5E-s1103556--f9da7bb2e0a273cdcd91eddad394d921.nii.gz \ No newline at end of file diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index a09821fd1..000000000 --- a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:45:55.827500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999316, - -0.0313383, - 0.0196295, - 0.036294, - 0.932881, - -0.358352 - ], - "ImageOrientationText": "Tra>Cor(-21.0)>Sag(0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0830488, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 605, - -7271, - -8809, - 436, - 29, - -353, - -24, - 33 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 321.111, - "WipMemBlock": "4d560d25-d2d2-4b67-ad19-ebed45369c9b||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 448af1337..000000000 --- a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/9K/P9/MD5E-s1103718--e862f1a8c9809ac71e4395d07f39da9f.nii.gz/MD5E-s1103718--e862f1a8c9809ac71e4395d07f39da9f.nii.gz \ No newline at end of file diff --git a/sub-05/ses-001/sub-05_ses-001_scans.tsv b/sub-05/ses-001/sub-05_ses-001_scans.tsv index ce394ee9c..2cf38422d 120000 --- a/sub-05/ses-001/sub-05_ses-001_scans.tsv +++ b/sub-05/ses-001/sub-05_ses-001_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/gw/Fx/MD5E-s3289--0c9911e9438d80927952b4febfb1fc68.tsv/MD5E-s3289--0c9911e9438d80927952b4febfb1fc68.tsv \ No newline at end of file +../../.git/annex/objects/0q/vM/MD5E-s2567--a5feb18e0014985d4a5965c50e48c4ab.tsv/MD5E-s2567--a5feb18e0014985d4a5965c50e48c4ab.tsv \ No newline at end of file From 086a4f20f73b4b76383267f9ad4ea1a0890f36dc Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:02:12 -0400 Subject: [PATCH 273/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..ba431d3aa --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = ee9b6383-867b-43d7-8ffa-1b805577fcbc diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..a57b8425f --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit a57b8425fa178fe61fb0bccaa3d9ac5aef04f8da From 871dc9f8b2ec0133a2e4ea2be02219aaa7fea7c2 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:02:16 -0400 Subject: [PATCH 274/463] fix complex event files --- ...g_events.tsv => sub-05_ses-001_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-05_ses-001_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-05_ses-001_task-mario3_run-03_events.tsv} | 0 .../func/sub-05_ses-001_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-05_ses-001_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-05_ses-001_task-mario3_run-04_events.tsv} | 0 .../func/sub-05_ses-001_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-05_ses-001_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-05/ses-001/func/{sub-05_ses-001_task-mario3_run-01_part-mag_events.tsv => sub-05_ses-001_task-mario3_run-01_events.tsv} (100%) rename sub-05/ses-001/func/{sub-05_ses-001_task-mario3_run-01_part-phase_events.tsv => sub-05_ses-001_task-mario3_run-02_events.tsv} (100%) rename sub-05/ses-001/func/{sub-05_ses-001_task-mario3_run-02_part-mag_events.tsv => sub-05_ses-001_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_part-phase_events.tsv rename sub-05/ses-001/func/{sub-05_ses-001_task-mario3_run-02_part-phase_events.tsv => sub-05_ses-001_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-01_part-mag_events.tsv b/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-01_events.tsv similarity index 100% rename from sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-01_part-mag_events.tsv rename to sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-01_events.tsv diff --git a/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-01_part-phase_events.tsv b/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_events.tsv similarity index 100% rename from sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-01_part-phase_events.tsv rename to sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_events.tsv diff --git a/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_part-mag_events.tsv b/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_events.tsv similarity index 100% rename from sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_part-mag_events.tsv rename to sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_events.tsv diff --git a/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_part-mag_events.tsv b/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_part-phase_events.tsv b/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_part-phase_events.tsv b/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_events.tsv similarity index 100% rename from sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_part-phase_events.tsv rename to sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_events.tsv diff --git a/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_part-mag_events.tsv b/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_part-phase_events.tsv b/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From c799d67601b06a6d537297b55250a209a438f76f Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:02:37 -0400 Subject: [PATCH 275/463] fix fmap phase --- ...6_ses-006_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-006_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-006_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-06/ses-006/sub-06_ses-006_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-06/ses-006/fmap/{sub-06_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-06_ses-006_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-006/fmap/{sub-06_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-006_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-006/fmap/{sub-06_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-06_ses-006_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-006/fmap/{sub-06_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-006_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-006/fmap/{sub-06_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-06_ses-006_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-06/ses-006/fmap/{sub-06_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-06_ses-006_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-06/ses-006/fmap/{sub-06_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-06_ses-006_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-06/ses-006/fmap/{sub-06_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-06_ses-006_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-06/ses-006/fmap/{sub-06_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-06_ses-006_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-06/ses-006/fmap/{sub-06_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-06_ses-006_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index a806883f0..000000000 --- a/sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:23:1.335000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.99817, -0.0595147, 0.0107347, 0.0598267, 0.945864, -0.319], - "ImageOrientationText": "Tra>Cor(-18.6)>Sag(-0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0714664, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [624, -7265, -8834, 536, 26, -252, -53, -8], - "SliceThickness": 2, - "SliceTiming": [0, 0.7825, 0.0975, 0.88, 0.195, 0.9775, 0.2925, 1.0775, 0.39, 1.175, 0.4875, 1.2725, 0.5875, 1.37, 0.685, 0, 0.7825, 0.0975, 0.88, 0.195, 0.9775, 0.2925, 1.0775, 0.39, 1.175, 0.4875, 1.2725, 0.5875, 1.37, 0.685, 0, 0.7825, 0.0975, 0.88, 0.195, 0.9775, 0.2925, 1.0775, 0.39, 1.175, 0.4875, 1.2725, 0.5875, 1.37, 0.685, 0, 0.7825, 0.0975, 0.88, 0.195, 0.9775, 0.2925, 1.0775, 0.39, 1.175, 0.4875, 1.2725, 0.5875, 1.37, 0.685], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 314.074, - "WipMemBlock": "d3806101-1a8e-4de8-bdbd-928a89536836||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9963394403457642, 0.11965342611074448, -0.017663218080997467, 100.93151092529297], - [0.11902938783168793, 1.8917289972305298, -0.6381170153617859, -72.47587585449219], - [0.02146943286061287, 0.6380003094673157, 1.8953876495361328, -65.78069305419922], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.9981697086213, -0.0595146928104, 0.01073471613804, 0.05982671199899, 0.94586450688841, -0.319000155392], - "ImagePositionPatient": [-883.47721099913, -767.63487690169, 224.35057897983], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.259018, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "162056.058000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.07146642952345, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "162347.353000", - "SliceLocation": -40.107301459735, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999469862, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "162055.987000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["162301.335000", "162302.825000", "162304.315000"], - "ContentTime": ["162347.355000", "162347.358000", "162347.361000"], - "InstanceCreationTime": ["162347.355000", "162347.358000", "162347.361000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4766.0, 4772.0, 4764.0], - "WindowWidth": [18530.0, 18524.0, 18526.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index d53ba3618..000000000 --- a/sub-06/ses-006/fmap/sub-06_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/KJ/KQ/MD5E-s3335112--b6c59cde7af53ece7bab7cb4771b4f8b.nii.gz/MD5E-s3335112--b6c59cde7af53ece7bab7cb4771b4f8b.nii.gz \ No newline at end of file diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index dd1ca80ec..000000000 --- a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:22:50.905000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99817, - -0.0595147, - 0.0107347, - 0.0598267, - 0.945864, - -0.319 - ], - "ImageOrientationText": "Tra>Cor(-18.6)>Sag(-0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0714664, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 624, - -7265, - -8834, - 536, - 26, - -252, - -53, - -8 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 314.074, - "WipMemBlock": "d3806101-1a8e-4de8-bdbd-928a89536836||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 09882649a..000000000 --- a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/M1/7K/MD5E-s1112262--57003e3687984c738ffec457d17404e2.nii.gz/MD5E-s1112262--57003e3687984c738ffec457d17404e2.nii.gz \ No newline at end of file diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index e16f05c91..000000000 --- a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:24:3.562500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99817, - -0.0595147, - 0.0107347, - 0.0598267, - 0.945864, - -0.319 - ], - "ImageOrientationText": "Tra>Cor(-18.6)>Sag(-0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0896126, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 624, - -7265, - -8834, - 536, - 26, - -252, - -53, - -8 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 314.074, - "WipMemBlock": "da299ac8-1cd7-4c72-9e12-eb1b4dbf8c35||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index ac7b19bda..000000000 --- a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Z8/3P/MD5E-s1103468--da2620408224859e85cad19edf73ebf1.nii.gz/MD5E-s1103468--da2620408224859e85cad19edf73ebf1.nii.gz \ No newline at end of file diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index d9b74b381..000000000 --- a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:36:30.132500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99817, - -0.0595147, - 0.0107347, - 0.0598267, - 0.945864, - -0.319 - ], - "ImageOrientationText": "Tra>Cor(-18.6)>Sag(-0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0896126, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 624, - -7265, - -8834, - 536, - 26, - -252, - -53, - -8 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 314.074, - "WipMemBlock": "31b3a6ed-0d64-4b68-8c1b-4c0f4d029b3a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 890679ec6..000000000 --- a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/pj/w1/MD5E-s1103378--bb2aaefa9bd97cba39b7e35ad8c021fa.nii.gz/MD5E-s1103378--bb2aaefa9bd97cba39b7e35ad8c021fa.nii.gz \ No newline at end of file diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index a47b250fe..000000000 --- a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:52:13.902500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99817, - -0.0595147, - 0.0107347, - 0.0598267, - 0.945864, - -0.319 - ], - "ImageOrientationText": "Tra>Cor(-18.6)>Sag(-0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0896126, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 624, - -7265, - -8834, - 536, - 26, - -252, - -53, - -8 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 314.074, - "WipMemBlock": "b5309ceb-6f6e-40ff-863f-47f55cd6dfe5||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 07c75d743..000000000 --- a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/M4/2m/MD5E-s1103413--4a62d9ea3294b68e1f873ed8def45f99.nii.gz/MD5E-s1103413--4a62d9ea3294b68e1f873ed8def45f99.nii.gz \ No newline at end of file diff --git a/sub-06/ses-006/sub-06_ses-006_scans.tsv b/sub-06/ses-006/sub-06_ses-006_scans.tsv index dc2ef60be..499d45a74 120000 --- a/sub-06/ses-006/sub-06_ses-006_scans.tsv +++ b/sub-06/ses-006/sub-06_ses-006_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/qQ/JF/MD5E-s2660--6cdcb84e2d7b3558ca37fed0f1e2983c.tsv/MD5E-s2660--6cdcb84e2d7b3558ca37fed0f1e2983c.tsv \ No newline at end of file +../../.git/annex/objects/Gv/f1/MD5E-s2059--8d5c4ec57f76c4dbe16fa02aa5d07f80.tsv/MD5E-s2059--8d5c4ec57f76c4dbe16fa02aa5d07f80.tsv \ No newline at end of file From ed9ce78d581bfe313c44d395b34dc7f2804f587c Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:02:37 -0400 Subject: [PATCH 276/463] fix fmap phase --- ...3_ses-014_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-014_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-014_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-014_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-014_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-014_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-014_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-014_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - sub-03/ses-014/sub-03_ses-014_scans.tsv | 2 +- 29 files changed, 1 insertion(+), 1097 deletions(-) rename sub-03/ses-014/fmap/{sub-03_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-014_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-014/fmap/{sub-03_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-014_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-014/fmap/sub-03_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-014/fmap/sub-03_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-014/fmap/{sub-03_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-014_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-014/fmap/{sub-03_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-014_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-014/fmap/{sub-03_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-014_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-014/fmap/{sub-03_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-014_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-014/fmap/{sub-03_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-014_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-014/fmap/{sub-03_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-014_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-03/ses-014/fmap/{sub-03_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-03_ses-014_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-03/ses-014/fmap/{sub-03_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-03_ses-014_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-03/ses-014/fmap/{sub-03_ses-014_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-03_ses-014_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-03/ses-014/fmap/{sub-03_ses-014_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-03_ses-014_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-03/ses-014/fmap/{sub-03_ses-014_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-03_ses-014_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-03/ses-014/fmap/{sub-03_ses-014_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-03_ses-014_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-014/fmap/sub-03_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-014/fmap/sub-03_ses-014_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-014/fmap/sub-03_ses-014_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-014/fmap/sub-03_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-014/fmap/sub-03_ses-014_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 9358cba6d..000000000 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:43:17.302500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999852, 0.0129256, 0.0113272, -0.00959816, 0.966669, -0.255848], - "ImageOrientationText": "Tra>Cor(-14.8)>Sag(0.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0451401, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [622, -7223, -8803, 712, 68, 4, 34, 0], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.08, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875, 0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.08, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875, 0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.08, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875, 0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.08, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.874, - "WipMemBlock": "1b6b0c33-7f9e-4977-bef3-efcc234f20f2||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9997045993804932, -0.01919631101191044, 0.028513208031654358, 108.95744323730469], - [-0.02585117518901825, 1.9333387613296509, -0.5114030241966248, -73.26385498046875], - [0.022654319182038307, 0.5116961002349854, 1.9333012104034424, -67.04470825195312], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.9998523014126, 0.01292558749325, 0.01132715974511, -0.0095981554396, 0.96666936233583, -0.255848039534], - "ImagePositionPatient": [-827.88524007602, -839.01515905492, 163.67118460645], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.260483, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "134057.758000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.04514009362976, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "134403.769000", - "SliceLocation": -44.521771778806, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999509724, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "134057.669000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["134317.302500", "134318.792500", "134320.282500"], - "ContentTime": ["134403.771000", "134403.792000", "134403.795000"], - "InstanceCreationTime": ["134403.771000", "134403.792000", "134403.795000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4772.0, 4794.0, 4770.0], - "WindowWidth": [18594.0, 18624.0, 18592.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-014/fmap/sub-03_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 55c8899eb..000000000 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/FW/Vv/MD5E-s3334544--e1f4080ac20500d0f4af590900bbcbec.nii.gz/MD5E-s3334544--e1f4080ac20500d0f4af590900bbcbec.nii.gz \ No newline at end of file diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index e0d506aa2..000000000 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:43:6.872500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999852, - 0.0129256, - 0.0113272, - -0.00959816, - 0.966669, - -0.255848 - ], - "ImageOrientationText": "Tra>Cor(-14.8)>Sag(0.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0451401, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 622, - -7223, - -8803, - 712, - 68, - 4, - 34, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.874, - "WipMemBlock": "1b6b0c33-7f9e-4977-bef3-efcc234f20f2||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 5f263bbc0..000000000 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/V2/X4/MD5E-s1112316--bc0a4bc9d239ec60f21dfb85bcc71bc6.nii.gz/MD5E-s1112316--bc0a4bc9d239ec60f21dfb85bcc71bc6.nii.gz \ No newline at end of file diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index de82c773a..000000000 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:44:7.255000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999852, - 0.0129256, - 0.0113272, - -0.00959816, - 0.966669, - -0.255848 - ], - "ImageOrientationText": "Tra>Cor(-14.8)>Sag(0.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0566017, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 622, - -7223, - -8803, - 712, - 68, - 4, - 34, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": 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sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 7b545f722..000000000 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:53:51.195000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999852, - 0.0129256, - 0.0113272, - -0.00959816, - 0.966669, - -0.255848 - ], - "ImageOrientationText": "Tra>Cor(-14.8)>Sag(0.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0566017, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 622, - -7223, - -8803, - 712, - 68, - 4, - 34, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.874, - "WipMemBlock": "bbe1e0cc-c26c-43c7-8795-fb5f311ab304||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 9d68900c6..000000000 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/fK/28/MD5E-s1103617--cc223fc3febad4caf44d13a17f3ccfd5.nii.gz/MD5E-s1103617--cc223fc3febad4caf44d13a17f3ccfd5.nii.gz \ No newline at end of file diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 7d626cac0..000000000 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:03:9.312500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999852, - 0.0129256, - 0.0113272, - -0.00959816, - 0.966669, - -0.255848 - ], - "ImageOrientationText": "Tra>Cor(-14.8)>Sag(0.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0566017, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 622, - -7223, - -8803, - 712, - 68, - 4, - 34, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.874, - "WipMemBlock": "d4ed91b5-5361-48cd-aee5-51b905639918||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 44833e17d..000000000 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/wF/J4/MD5E-s1103631--1a166210f7d7e12395c2400757be1432.nii.gz/MD5E-s1103631--1a166210f7d7e12395c2400757be1432.nii.gz \ No newline at end of file diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 54ae9a7cf..000000000 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:14:18.092500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999852, - 0.0129256, - 0.0113272, - -0.00959816, - 0.966669, - -0.255848 - ], - "ImageOrientationText": "Tra>Cor(-14.8)>Sag(0.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0566017, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 622, - -7223, - -8803, - 712, - 68, - 4, - 34, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.874, - "WipMemBlock": "68880c4d-a29b-42a3-925d-33a0704464d6||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 6fbec08aa..000000000 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/pg/0k/MD5E-s1103719--f449ccaae2d9929e8930ca877413eb95.nii.gz/MD5E-s1103719--f449ccaae2d9929e8930ca877413eb95.nii.gz \ No newline at end of file diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index fb3fabed5..000000000 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:23:43.180000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999852, - 0.0129256, - 0.0113272, - -0.00959816, - 0.966669, - -0.255848 - ], - "ImageOrientationText": "Tra>Cor(-14.8)>Sag(0.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-05", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0566017, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 622, - -7223, - -8803, - 712, - 68, - 4, - 34, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.874, - "WipMemBlock": "a38cf0f4-ad01-48da-8ff7-586ad732bd29||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index 1133d19ca..000000000 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/WP/47/MD5E-s1103628--fe4ada5f016f95ce4c114685e58b62ae.nii.gz/MD5E-s1103628--fe4ada5f016f95ce4c114685e58b62ae.nii.gz \ No newline at end of file diff --git a/sub-03/ses-014/sub-03_ses-014_scans.tsv b/sub-03/ses-014/sub-03_ses-014_scans.tsv index d69110c26..bf4431097 120000 --- a/sub-03/ses-014/sub-03_ses-014_scans.tsv +++ b/sub-03/ses-014/sub-03_ses-014_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/zW/wj/MD5E-s3911--dfedf36601f9b2bf01b7f7c0a5d272d8.tsv/MD5E-s3911--dfedf36601f9b2bf01b7f7c0a5d272d8.tsv \ No newline at end of file +../../.git/annex/objects/0Q/mF/MD5E-s3068--d9a002e210975b944bd102de1678da63.tsv/MD5E-s3068--d9a002e210975b944bd102de1678da63.tsv \ No newline at end of file From e53c36e602b086d11159fd615948e57c370072c2 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:02:46 -0400 Subject: [PATCH 277/463] fix complex event files --- ...g_events.tsv => sub-06_ses-006_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-06_ses-006_task-mario3_run-02_events.tsv} | 0 .../func/sub-06_ses-006_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-06_ses-006_task-mario3_run-03_events.tsv} | 0 .../func/sub-06_ses-006_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-06_ses-006_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-06/ses-006/func/{sub-06_ses-006_task-mario3_run-01_part-mag_events.tsv => sub-06_ses-006_task-mario3_run-01_events.tsv} (100%) rename sub-06/ses-006/func/{sub-06_ses-006_task-mario3_run-01_part-phase_events.tsv => sub-06_ses-006_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-02_part-phase_events.tsv rename sub-06/ses-006/func/{sub-06_ses-006_task-mario3_run-02_part-mag_events.tsv => sub-06_ses-006_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-01_part-mag_events.tsv b/sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-01_events.tsv similarity index 100% rename from sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-01_part-mag_events.tsv rename to sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-01_events.tsv diff --git a/sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-01_part-phase_events.tsv b/sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-02_events.tsv similarity index 100% rename from sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-01_part-phase_events.tsv rename to sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-02_events.tsv diff --git a/sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-02_part-phase_events.tsv b/sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-02_part-mag_events.tsv b/sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_events.tsv similarity index 100% rename from sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-02_part-mag_events.tsv rename to sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_events.tsv diff --git a/sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-mag_events.tsv b/sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-phase_events.tsv b/sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-006/func/sub-06_ses-006_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 2c3e456051238923bdd96c910655ea733006c41f Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:02:47 -0400 Subject: [PATCH 278/463] fix complex event files --- ...g_events.tsv => sub-03_ses-014_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-03_ses-014_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-03_ses-014_task-mario3_run-03_events.tsv} | 0 .../func/sub-03_ses-014_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-03_ses-014_task-mario3_run-04_events.tsv} | 0 .../func/sub-03_ses-014_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-03_ses-014_task-mario3_run-04_part-phase_events.tsv | 1 - ...g_events.tsv => sub-03_ses-014_task-mario3_run-05_events.tsv} | 0 .../func/sub-03_ses-014_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-03_ses-014_task-mario3_run-05_part-phase_events.tsv | 1 - 10 files changed, 5 deletions(-) rename sub-03/ses-014/func/{sub-03_ses-014_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-014_task-mario3_run-01_events.tsv} (100%) rename sub-03/ses-014/func/{sub-03_ses-014_task-mario3_run-01_part-phase_events.tsv => sub-03_ses-014_task-mario3_run-02_events.tsv} (100%) rename sub-03/ses-014/func/{sub-03_ses-014_task-mario3_run-02_part-mag_events.tsv => sub-03_ses-014_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-03_part-phase_events.tsv rename sub-03/ses-014/func/{sub-03_ses-014_task-mario3_run-02_part-phase_events.tsv => sub-03_ses-014_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-04_part-phase_events.tsv rename sub-03/ses-014/func/{sub-03_ses-014_task-mario3_run-03_part-mag_events.tsv => sub-03_ses-014_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-05_part-phase_events.tsv diff --git a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-02_events.tsv similarity index 100% rename from sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-01_part-phase_events.tsv rename to sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-02_events.tsv diff --git a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-02_part-mag_events.tsv b/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-03_events.tsv similarity index 100% rename from sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-02_part-mag_events.tsv rename to sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-03_events.tsv diff --git a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-03_part-phase_events.tsv b/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-02_part-phase_events.tsv b/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-04_events.tsv similarity index 100% rename from sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-02_part-phase_events.tsv rename to sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-04_events.tsv diff --git a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-04_part-mag_events.tsv b/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-04_part-phase_events.tsv b/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-03_part-mag_events.tsv b/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-05_events.tsv similarity index 100% rename from sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-03_part-mag_events.tsv rename to sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-05_events.tsv diff --git a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-05_part-mag_events.tsv b/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-05_part-phase_events.tsv b/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 2836701a71707b6c014b90d5c22f835b34b2a908 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:02:52 -0400 Subject: [PATCH 279/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-06_ses-005_acq-axial_localizer.json | 81 +++ .../sub-06_ses-005_acq-axial_localizer.nii.gz | 1 + .../sub-06_ses-005_acq-coronal_localizer.json | 81 +++ ...ub-06_ses-005_acq-coronal_localizer.nii.gz | 1 + ...sub-06_ses-005_acq-sagittal_localizer.json | 86 +++ ...b-06_ses-005_acq-sagittal_localizer.nii.gz | 1 + sub-06/ses-005/anat/sub-06_ses-005_scout.json | 542 ++++++++++++++++++ .../ses-005/anat/sub-06_ses-005_scout.nii.gz | 1 + ...5_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-005_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...05_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...005_task-mario3_run-01_part-mag_events.tsv | 1 + ...005_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...05_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-01_part-phase_events.tsv | 1 + ...5_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-005_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...05_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...005_task-mario3_run-02_part-mag_events.tsv | 1 + ...005_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...05_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-02_part-phase_events.tsv | 1 + ...5_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-005_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...05_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...005_task-mario3_run-03_part-mag_events.tsv | 1 + ...005_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...05_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-03_part-phase_events.tsv | 1 + ...5_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-06/ses-005/sub-06_ses-005_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-06/ses-005/anat/sub-06_ses-005_acq-axial_localizer.json create mode 120000 sub-06/ses-005/anat/sub-06_ses-005_acq-axial_localizer.nii.gz create mode 100644 sub-06/ses-005/anat/sub-06_ses-005_acq-coronal_localizer.json create mode 120000 sub-06/ses-005/anat/sub-06_ses-005_acq-coronal_localizer.nii.gz create mode 100644 sub-06/ses-005/anat/sub-06_ses-005_acq-sagittal_localizer.json create mode 120000 sub-06/ses-005/anat/sub-06_ses-005_acq-sagittal_localizer.nii.gz create mode 100644 sub-06/ses-005/anat/sub-06_ses-005_scout.json create mode 120000 sub-06/ses-005/anat/sub-06_ses-005_scout.nii.gz create mode 100644 sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-06/ses-005/sub-06_ses-005_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index a57b8425f..205d7512d 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit a57b8425fa178fe61fb0bccaa3d9ac5aef04f8da +Subproject commit 205d7512de411bff84a80468461774a47bf0816d diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..db37a3f34 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-06 41 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-06/ses-005/anat/sub-06_ses-005_acq-axial_localizer.json b/sub-06/ses-005/anat/sub-06_ses-005_acq-axial_localizer.json new file mode 100644 index 000000000..45146c9b1 --- /dev/null +++ b/sub-06/ses-005/anat/sub-06_ses-005_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:45:25.057500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + 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newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..2987674c5 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999287, -0.0377577, 0.000458971, 0.035769, 0.942619, -0.331948], + 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"ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [618, -7254, -8843, 562, 8, -232, -47, -34], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 271.29, + "dcmmeta_affine": [ + [-1.998573660850525, 0.07153793424367905, -0.02420191653072834, 103.03850555419922], + [0.07551533728837967, 1.8852382898330688, -0.6634559631347656, -68.8121566772461], + [0.0009179428452625871, 0.6638966202735901, 1.8865948915481567, -73.0420150756836], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From cc46e4637268c9d98542c7d08ab4a94fea911956 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:03:00 -0400 Subject: [PATCH 280/463] fix fmap phase --- ...6_ses-003_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-003_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-003_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-06/ses-003/sub-06_ses-003_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-06/ses-003/fmap/{sub-06_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-06_ses-003_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-003/fmap/{sub-06_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-003_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-003/fmap/{sub-06_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-06_ses-003_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-003/fmap/{sub-06_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-003_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-003/fmap/{sub-06_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-06_ses-003_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-06/ses-003/fmap/{sub-06_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-06_ses-003_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-06/ses-003/fmap/{sub-06_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-06_ses-003_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-06/ses-003/fmap/{sub-06_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-06_ses-003_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-06/ses-003/fmap/{sub-06_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-06_ses-003_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-06/ses-003/fmap/{sub-06_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-06_ses-003_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-06/ses-003/fmap/{sub-06_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-06_ses-003_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-06/ses-003/fmap/{sub-06_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-06_ses-003_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index f639cdf73..000000000 --- a/sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:10:12.532500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.998388, -0.055579, 0.0114739, 0.056343, 0.946541, -0.317624], - "ImageOrientationText": "Tra>Cor(-18.5)>Sag(-0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0335106, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [629, -7278, -8798, 571, 1, -235, -32, -8], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.156, - "WipMemBlock": "90102c84-653a-46c7-846f-d2e7f3ad4224||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9967767000198364, 0.11268598586320877, -0.013585363514721394, 100.61431884765625], - [0.11115794628858566, 1.8930823802947998, -0.6355177760124207, -71.58369445800781], - [0.022947870194911957, 0.6352486610412598, 1.896294355392456, -56.14326095581055], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99838836457, -0.0555789736469, 0.01147393479143, 0.05634299393489, 0.94654120705503, -0.3176243227167], - "ImagePositionPatient": [-880.06540091297, -772.02429729653, 232.16483279107], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.258752, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "160819.735000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.0335106152708, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "161058.393000", - "SliceLocation": -31.16915945575, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.999999961331, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "160819.655000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["161012.532500", "161014.022500", "161015.512500"], - "ContentTime": ["161058.395000", "161058.398000", "161058.400000"], - "InstanceCreationTime": ["161058.395000", "161058.398000", "161058.400000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4884.0, 4860.0, 4858.0], - "WindowWidth": [18724.0, 18692.0, 18694.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 2ece9f8c4..000000000 --- a/sub-06/ses-003/fmap/sub-06_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/F3/X3/MD5E-s3334793--c95b7f54dda4fce182073c78c597623b.nii.gz/MD5E-s3334793--c95b7f54dda4fce182073c78c597623b.nii.gz \ No newline at end of file diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index aada29953..000000000 --- a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:10:2.102500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998388, - -0.055579, - 0.0114739, - 0.056343, - 0.946541, - -0.317624 - ], - "ImageOrientationText": "Tra>Cor(-18.5)>Sag(-0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0335106, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 629, - -7278, - -8798, - 571, - 1, - -235, - -32, - -8 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.156, - "WipMemBlock": "90102c84-653a-46c7-846f-d2e7f3ad4224||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 3ff7a0a56..000000000 --- a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/jV/PW/MD5E-s1112378--c0c926f51f0ebfb8bc8cb018bca900bc.nii.gz/MD5E-s1112378--c0c926f51f0ebfb8bc8cb018bca900bc.nii.gz \ No newline at end of file diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 6d73c26b5..000000000 --- a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:11:49.282500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": 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"SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.156, - "WipMemBlock": "f12ceabb-5a4f-4f1f-bcec-cc78e6027c1f||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 04f45a2fb..000000000 --- a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Qj/v6/MD5E-s1103748--148a5de675bd3fca06769ab37f6f72a8.nii.gz/MD5E-s1103748--148a5de675bd3fca06769ab37f6f72a8.nii.gz \ No newline at end of file diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 683068506..000000000 --- a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:20:27.567500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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"PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0420194, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 629, - -7278, - -8798, - 571, - 1, - -235, - -32, - -8 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 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-../../../.git/annex/objects/mx/MP/MD5E-s1103434--99ce4498e2d2872f308c2d9bd3f1b1d3.nii.gz/MD5E-s1103434--99ce4498e2d2872f308c2d9bd3f1b1d3.nii.gz \ No newline at end of file diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 6a2d005b1..000000000 --- a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:30:43.270000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.156, - "WipMemBlock": "0e0c0d00-0fd0-4c53-ac38-e898ecb15bbf||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 9638fe47f..000000000 --- a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/K7/Kz/MD5E-s1103593--f47258464ce91437dc51661a2eac2bd1.nii.gz/MD5E-s1103593--f47258464ce91437dc51661a2eac2bd1.nii.gz \ No newline at end of file diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index b38c82d27..000000000 --- a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:39:1.065000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998388, - -0.055579, - 0.0114739, - 0.056343, - 0.946541, - -0.317624 - ], - "ImageOrientationText": "Tra>Cor(-18.5)>Sag(-0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0420194, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 629, - -7278, - -8798, - 571, - 1, - -235, - -32, - -8 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.156, - "WipMemBlock": "ccb66035-13c7-404f-8603-78cbc2bb82d9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 009953d4a..000000000 --- a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Vk/0M/MD5E-s1103448--693e836c950a0e07a4be5a6e7d779704.nii.gz/MD5E-s1103448--693e836c950a0e07a4be5a6e7d779704.nii.gz \ No newline at end of file diff --git a/sub-06/ses-003/sub-06_ses-003_scans.tsv b/sub-06/ses-003/sub-06_ses-003_scans.tsv index 874136f75..b51bc3aa5 120000 --- a/sub-06/ses-003/sub-06_ses-003_scans.tsv +++ b/sub-06/ses-003/sub-06_ses-003_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/9P/Qm/MD5E-s3289--318b5277782b40d20597c59c43d69c01.tsv/MD5E-s3289--318b5277782b40d20597c59c43d69c01.tsv \ No newline at end of file +../../.git/annex/objects/72/mv/MD5E-s2567--2deef64ef45bcd9f544abffc9a775311.tsv/MD5E-s2567--2deef64ef45bcd9f544abffc9a775311.tsv \ No newline at end of file From e581b6ac762828747ff67a5198e7edf62c57bdef Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:03:11 -0400 Subject: [PATCH 281/463] fix complex event files --- ...g_events.tsv => sub-06_ses-003_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-06_ses-003_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-06_ses-003_task-mario3_run-03_events.tsv} | 0 .../func/sub-06_ses-003_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-06_ses-003_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-06_ses-003_task-mario3_run-04_events.tsv} | 0 .../func/sub-06_ses-003_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-06_ses-003_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-06/ses-003/func/{sub-06_ses-003_task-mario3_run-01_part-mag_events.tsv => sub-06_ses-003_task-mario3_run-01_events.tsv} (100%) rename sub-06/ses-003/func/{sub-06_ses-003_task-mario3_run-01_part-phase_events.tsv => sub-06_ses-003_task-mario3_run-02_events.tsv} (100%) rename sub-06/ses-003/func/{sub-06_ses-003_task-mario3_run-02_part-mag_events.tsv => sub-06_ses-003_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_part-phase_events.tsv rename sub-06/ses-003/func/{sub-06_ses-003_task-mario3_run-02_part-phase_events.tsv => sub-06_ses-003_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-01_part-mag_events.tsv b/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-01_events.tsv similarity index 100% rename from sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-01_part-mag_events.tsv rename to sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-01_events.tsv diff --git a/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-01_part-phase_events.tsv b/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-02_events.tsv similarity index 100% rename from sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-01_part-phase_events.tsv rename to sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-02_events.tsv diff --git a/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-02_part-mag_events.tsv b/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_events.tsv similarity index 100% rename from sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-02_part-mag_events.tsv rename to sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_events.tsv diff --git a/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_part-mag_events.tsv b/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_part-phase_events.tsv b/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-02_part-phase_events.tsv b/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_events.tsv similarity index 100% rename from sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-02_part-phase_events.tsv rename to sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_events.tsv diff --git a/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-mag_events.tsv b/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-phase_events.tsv b/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-003/func/sub-06_ses-003_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 7e7b743675257022c074f0e27f3ded8bce3f9e40 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:03:55 -0400 Subject: [PATCH 282/463] fix fmap phase --- ...6_ses-005_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-005_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-005_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-005_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-005_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-005_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-005_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-06/ses-005/sub-06_ses-005_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-06/ses-005/fmap/{sub-06_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-06_ses-005_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-005/fmap/{sub-06_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-005_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-005/fmap/{sub-06_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-06_ses-005_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-005/fmap/{sub-06_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-005_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-005/fmap/{sub-06_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-06_ses-005_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-06/ses-005/fmap/{sub-06_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-06_ses-005_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-06/ses-005/fmap/{sub-06_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-06_ses-005_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-06/ses-005/fmap/{sub-06_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-06_ses-005_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-06/ses-005/fmap/{sub-06_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-06_ses-005_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-06/ses-005/fmap/{sub-06_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-06_ses-005_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 525d96df7..000000000 --- a/sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:46:26.367500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999287, -0.0377577, 0.000458971, 0.035769, 0.942619, -0.331948], - "ImageOrientationText": "Tra>Cor(-19.4)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0522736, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [618, -7254, -8843, 562, 8, -232, -47, -34], - "SliceThickness": 2, - "SliceTiming": [0, 0.7825, 0.0975, 0.88, 0.195, 0.98, 0.2925, 1.0775, 0.39, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685, 0, 0.7825, 0.0975, 0.88, 0.195, 0.98, 0.2925, 1.0775, 0.39, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685, 0, 0.7825, 0.0975, 0.88, 0.195, 0.98, 0.2925, 1.0775, 0.39, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685, 0, 0.7825, 0.0975, 0.88, 0.195, 0.98, 0.2925, 1.0775, 0.39, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 271.29, - "WipMemBlock": "812c9672-2240-48fd-a47a-a3940f5b610a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.998573660850525, 0.07153793424367905, -0.02420191653072834, 103.03850555419922], - [0.07551533728837967, 1.8852382898330688, -0.6634559631347656, -68.8121566772461], - [0.0009179428452625871, 0.6638966202735901, 1.8865948915481567, -73.0420150756836], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 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"AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["154626.367500", "154627.857500", "154629.347500"], - "ContentTime": ["154713.668000", "154713.670000", "154713.673000"], - "InstanceCreationTime": ["154713.668000", "154713.670000", "154713.673000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4744.0, 4744.0, 4742.0], - "WindowWidth": [18486.0, 18492.0, 18500.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 12ce730ba..000000000 --- a/sub-06/ses-005/fmap/sub-06_ses-005_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/6x/8V/MD5E-s3334470--7ff1d5ce5dd42fda8ac6b81a3320ca45.nii.gz/MD5E-s3334470--7ff1d5ce5dd42fda8ac6b81a3320ca45.nii.gz \ No newline at end of file diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 637ddaf2c..000000000 --- a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:46:15.937500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999287, - -0.0377577, - 0.000458971, - 0.035769, - 0.942619, - -0.331948 - ], - "ImageOrientationText": "Tra>Cor(-19.4)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0522736, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 618, - -7254, - -8843, - 562, - 8, - -232, - -47, - -34 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 271.29, - "WipMemBlock": "812c9672-2240-48fd-a47a-a3940f5b610a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index dad8142e9..000000000 --- a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/pP/wV/MD5E-s1112382--23c0ae7769215def38246d68a23d6fd1.nii.gz/MD5E-s1112382--23c0ae7769215def38246d68a23d6fd1.nii.gz \ No newline at end of file diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index c7eb577c1..000000000 --- a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:49:42.702500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999287, - -0.0377577, - 0.000458971, - 0.035769, - 0.942619, - -0.331948 - ], - "ImageOrientationText": "Tra>Cor(-19.4)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0655465, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 618, - -7254, - -8843, - 562, - 8, - -232, - -47, - -34 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 271.29, - "WipMemBlock": "a8ca7558-552d-4c14-b8d6-d28fd5b85b8d||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 30917ee28..000000000 --- a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/mx/29/MD5E-s1103338--e5e6eef95a6183644952e9ecddfadf16.nii.gz/MD5E-s1103338--e5e6eef95a6183644952e9ecddfadf16.nii.gz \ No newline at end of file diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index de842281c..000000000 --- a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:04:20.900000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999287, - -0.0377577, - 0.000458971, - 0.035769, - 0.942619, - -0.331948 - ], - "ImageOrientationText": "Tra>Cor(-19.4)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0655465, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 618, - -7254, - -8843, - 562, - 8, - -232, - -47, - -34 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 271.29, - "WipMemBlock": "a1a10a4f-6422-4e77-9393-506dd19069f2||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 5a13f00ed..000000000 --- a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Xf/zk/MD5E-s1103547--f7f0254a9d9d117dd92091bdb38d5c59.nii.gz/MD5E-s1103547--f7f0254a9d9d117dd92091bdb38d5c59.nii.gz \ No newline at end of file diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index f7f1a02d2..000000000 --- a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:16:36.045000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999287, - -0.0377577, - 0.000458971, - 0.035769, - 0.942619, - -0.331948 - ], - "ImageOrientationText": "Tra>Cor(-19.4)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0655465, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 618, - -7254, - -8843, - 562, - 8, - -232, - -47, - -34 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 271.29, - "WipMemBlock": "7c78bf00-5b22-4313-b656-0a10163acf41||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 36514d8cc..000000000 --- a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/z9/pP/MD5E-s1103532--09fef58d8565508a1caabf0f3f81c0e0.nii.gz/MD5E-s1103532--09fef58d8565508a1caabf0f3f81c0e0.nii.gz \ No newline at end of file diff --git a/sub-06/ses-005/sub-06_ses-005_scans.tsv b/sub-06/ses-005/sub-06_ses-005_scans.tsv index 30eb1e5ec..9034108b6 120000 --- a/sub-06/ses-005/sub-06_ses-005_scans.tsv +++ b/sub-06/ses-005/sub-06_ses-005_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/6G/0z/MD5E-s2660--6de1d5e2e8823d773561c355fd972522.tsv/MD5E-s2660--6de1d5e2e8823d773561c355fd972522.tsv \ No newline at end of file +../../.git/annex/objects/K9/xw/MD5E-s2059--462fbb9cec3598ef3c8e564eb9c71052.tsv/MD5E-s2059--462fbb9cec3598ef3c8e564eb9c71052.tsv \ No newline at end of file From 5173a0bd75737aa26dae5e2a848d472d5e06954b Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:04:07 -0400 Subject: [PATCH 283/463] fix complex event files --- ...g_events.tsv => sub-06_ses-005_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-06_ses-005_task-mario3_run-02_events.tsv} | 0 .../func/sub-06_ses-005_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-06_ses-005_task-mario3_run-03_events.tsv} | 0 .../func/sub-06_ses-005_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-06_ses-005_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-06/ses-005/func/{sub-06_ses-005_task-mario3_run-01_part-mag_events.tsv => sub-06_ses-005_task-mario3_run-01_events.tsv} (100%) rename sub-06/ses-005/func/{sub-06_ses-005_task-mario3_run-01_part-phase_events.tsv => sub-06_ses-005_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-02_part-phase_events.tsv rename sub-06/ses-005/func/{sub-06_ses-005_task-mario3_run-02_part-mag_events.tsv => sub-06_ses-005_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-01_part-mag_events.tsv b/sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-01_events.tsv similarity index 100% rename from sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-01_part-mag_events.tsv rename to sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-01_events.tsv diff --git a/sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-01_part-phase_events.tsv b/sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-02_events.tsv similarity index 100% rename from sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-01_part-phase_events.tsv rename to sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-02_events.tsv diff --git a/sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-02_part-phase_events.tsv b/sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-02_part-mag_events.tsv b/sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_events.tsv similarity index 100% rename from sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-02_part-mag_events.tsv rename to sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_events.tsv diff --git a/sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_part-mag_events.tsv b/sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_part-phase_events.tsv b/sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-005/func/sub-06_ses-005_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 99b76a30b8d80acc40f4d7f77410e32894aa23d4 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:05:38 -0400 Subject: [PATCH 284/463] fill IntendedFor --- ...5_ses-001_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...5_ses-001_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...5_ses-001_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...5_ses-001_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...5_ses-001_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_epi.json b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_epi.json index 8890923c3..9fe905980 100644 --- a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999316, - -0.0313383, - 0.0196295, - 0.036294, - 0.932881, - -0.358352 - ], + "ImageOrientationPatientDICOM": [0.999316, -0.0313383, 0.0196295, 0.036294, 0.932881, -0.358352], "ImageOrientationText": "Tra>Cor(-21.0)>Sag(0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-05_ses-001_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-001/func/sub-05_ses-001_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-001/func/sub-05_ses-001_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-001/func/sub-05_ses-001_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 605, - -7271, - -8809, - 436, - 29, - -353, - -24, - 33 - ], + "ShimSetting": [605, -7271, -8809, 436, 29, -353, -24, 33], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_epi.json b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_epi.json index af4a56d42..206b84307 100644 --- a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999316, - -0.0313383, - 0.0196295, - 0.036294, - 0.932881, - -0.358352 - ], + "ImageOrientationPatientDICOM": [0.999316, -0.0313383, 0.0196295, 0.036294, 0.932881, -0.358352], "ImageOrientationText": "Tra>Cor(-21.0)>Sag(0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-05_ses-001_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 605, - -7271, - -8809, - 436, - 29, - -353, - -24, - 33 - ], + "ShimSetting": [605, -7271, -8809, 436, 29, -353, -24, 33], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_epi.json b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_epi.json index 48967740f..dbdd841e5 100644 --- a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999316, - -0.0313383, - 0.0196295, - 0.036294, - 0.932881, - -0.358352 - ], + "ImageOrientationPatientDICOM": [0.999316, -0.0313383, 0.0196295, 0.036294, 0.932881, -0.358352], "ImageOrientationText": "Tra>Cor(-21.0)>Sag(0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-05_ses-001_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 605, - -7271, - -8809, - 436, - 29, - -353, - -24, - 33 - ], + "ShimSetting": [605, -7271, -8809, 436, 29, -353, -24, 33], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_epi.json b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_epi.json index cb1960144..b741bcd79 100644 --- a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999316, - -0.0313383, - 0.0196295, - 0.036294, - 0.932881, - -0.358352 - ], + "ImageOrientationPatientDICOM": [0.999316, -0.0313383, 0.0196295, 0.036294, 0.932881, -0.358352], "ImageOrientationText": "Tra>Cor(-21.0)>Sag(0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-05_ses-001_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 605, - -7271, - -8809, - 436, - 29, - -353, - -24, - 33 - ], + "ShimSetting": [605, -7271, -8809, 436, 29, -353, -24, 33], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_epi.json b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_epi.json index aa51cf437..3a3699a6f 100644 --- a/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-05/ses-001/fmap/sub-05_ses-001_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999316, - -0.0313383, - 0.0196295, - 0.036294, - 0.932881, - -0.358352 - ], + "ImageOrientationPatientDICOM": [0.999316, -0.0313383, 0.0196295, 0.036294, 0.932881, -0.358352], "ImageOrientationText": "Tra>Cor(-21.0)>Sag(0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-05_ses-001_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 605, - -7271, - -8809, - 436, - 29, - -353, - -24, - 33 - ], + "ShimSetting": [605, -7271, -8809, 436, 29, -353, -24, 33], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From d14b17456ac60b4aac420f17c0788e540edf45d1 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:05:49 -0400 Subject: [PATCH 285/463] fill IntendedFor --- ...6_ses-006_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...6_ses-006_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...6_ses-006_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...6_ses-006_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_epi.json b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_epi.json index 56202beeb..4357f48c3 100644 --- a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99817, - -0.0595147, - 0.0107347, - 0.0598267, - 0.945864, - -0.319 - ], + "ImageOrientationPatientDICOM": [0.99817, -0.0595147, 0.0107347, 0.0598267, 0.945864, -0.319], "ImageOrientationText": "Tra>Cor(-18.6)>Sag(-0.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-06_ses-006_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-006/func/sub-06_ses-006_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-006/func/sub-06_ses-006_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 624, - -7265, - -8834, - 536, - 26, - -252, - -53, - -8 - ], + "ShimSetting": [624, -7265, -8834, 536, 26, -252, -53, -8], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.4875, 0.5875, 0.685, 0.7825, 0.88, 0.9775, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.485, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_epi.json b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_epi.json index d2a85c4c0..c3e05903c 100644 --- a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99817, - -0.0595147, - 0.0107347, - 0.0598267, - 0.945864, - -0.319 - ], + "ImageOrientationPatientDICOM": [0.99817, -0.0595147, 0.0107347, 0.0598267, 0.945864, -0.319], "ImageOrientationText": "Tra>Cor(-18.6)>Sag(-0.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-06_ses-006_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 624, - -7265, - -8834, - 536, - 26, - -252, - -53, - -8 - ], + "ShimSetting": [624, -7265, -8834, 536, 26, -252, -53, -8], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_epi.json b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_epi.json index 4e0f1ee37..fc64c8d58 100644 --- a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99817, - -0.0595147, - 0.0107347, - 0.0598267, - 0.945864, - -0.319 - ], + "ImageOrientationPatientDICOM": [0.99817, -0.0595147, 0.0107347, 0.0598267, 0.945864, -0.319], "ImageOrientationText": "Tra>Cor(-18.6)>Sag(-0.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-06_ses-006_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 624, - -7265, - -8834, - 536, - 26, - -252, - -53, - -8 - ], + "ShimSetting": [624, -7265, -8834, 536, 26, -252, -53, -8], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_epi.json b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_epi.json index 4e66aebcd..a8353a10a 100644 --- a/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-06/ses-006/fmap/sub-06_ses-006_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99817, - -0.0595147, - 0.0107347, - 0.0598267, - 0.945864, - -0.319 - ], + "ImageOrientationPatientDICOM": [0.99817, -0.0595147, 0.0107347, 0.0598267, 0.945864, -0.319], "ImageOrientationText": "Tra>Cor(-18.6)>Sag(-0.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-06_ses-006_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 624, - -7265, - -8834, - 536, - 26, - -252, - -53, - -8 - ], + "ShimSetting": [624, -7265, -8834, 536, 26, -252, -53, -8], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 44984d149135e9cc532fab3a633e39803c63eb20 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:06:09 -0400 Subject: [PATCH 286/463] fill IntendedFor --- ...3_ses-014_acq-sbref_dir-AP_run-01_epi.json | 92 +++---------------- ...3_ses-014_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...3_ses-014_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...3_ses-014_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...3_ses-014_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- ...3_ses-014_acq-sbref_dir-PA_run-05_epi.json | 88 ++---------------- 6 files changed, 46 insertions(+), 486 deletions(-) diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_epi.json index 216bcd310..da1d96159 100644 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999852, - 0.0129256, - 0.0113272, - -0.00959816, - 0.966669, - -0.255848 - ], + "ImageOrientationPatientDICOM": [0.999852, 0.0129256, 0.0113272, -0.00959816, 0.966669, -0.255848], "ImageOrientationText": "Tra>Cor(-14.8)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,19 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-03_ses-014_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-014/func/sub-03_ses-014_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-014/func/sub-03_ses-014_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-014/func/sub-03_ses-014_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-014/func/sub-03_ses-014_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +67,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 622, - -7223, - -8803, - 712, - 68, - 4, - 34, - 0 - ], + "ShimSetting": [622, -7223, -8803, 712, 68, 4, 34, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.02, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_epi.json index afdb83c90..931fce5a9 100644 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999852, - 0.0129256, - 0.0113272, - -0.00959816, - 0.966669, - -0.255848 - ], + "ImageOrientationPatientDICOM": [0.999852, 0.0129256, 0.0113272, -0.00959816, 0.966669, -0.255848], "ImageOrientationText": "Tra>Cor(-14.8)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-03_ses-014_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 622, - -7223, - -8803, - 712, - 68, - 4, - 34, - 0 - ], + "ShimSetting": [622, -7223, -8803, 712, 68, 4, 34, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_epi.json index e19b8a01a..863f4740f 100644 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999852, - 0.0129256, - 0.0113272, - -0.00959816, - 0.966669, - -0.255848 - ], + "ImageOrientationPatientDICOM": [0.999852, 0.0129256, 0.0113272, -0.00959816, 0.966669, -0.255848], "ImageOrientationText": "Tra>Cor(-14.8)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-03_ses-014_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 622, - -7223, - -8803, - 712, - 68, - 4, - 34, - 0 - ], + "ShimSetting": [622, -7223, -8803, 712, 68, 4, 34, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_epi.json index 1d2454679..ecad31a24 100644 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999852, - 0.0129256, - 0.0113272, - -0.00959816, - 0.966669, - -0.255848 - ], + "ImageOrientationPatientDICOM": [0.999852, 0.0129256, 0.0113272, -0.00959816, 0.966669, -0.255848], "ImageOrientationText": "Tra>Cor(-14.8)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-03_ses-014_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 622, - -7223, - -8803, - 712, - 68, - 4, - 34, - 0 - ], + "ShimSetting": [622, -7223, -8803, 712, 68, 4, 34, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_epi.json index bdc744c36..13720b042 100644 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999852, - 0.0129256, - 0.0113272, - -0.00959816, - 0.966669, - -0.255848 - ], + "ImageOrientationPatientDICOM": [0.999852, 0.0129256, 0.0113272, -0.00959816, 0.966669, -0.255848], "ImageOrientationText": "Tra>Cor(-14.8)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-03_ses-014_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 622, - -7223, - -8803, - 712, - 68, - 4, - 34, - 0 - ], + "ShimSetting": [622, -7223, -8803, 712, 68, 4, 34, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_epi.json b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_epi.json index dcac5d016..1af4ef294 100644 --- a/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-03/ses-014/fmap/sub-03_ses-014_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999852, - 0.0129256, - 0.0113272, - -0.00959816, - 0.966669, - -0.255848 - ], + "ImageOrientationPatientDICOM": [0.999852, 0.0129256, 0.0113272, -0.00959816, 0.966669, -0.255848], "ImageOrientationText": "Tra>Cor(-14.8)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-03_ses-014_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 622, - -7223, - -8803, - 712, - 68, - 4, - 34, - 0 - ], + "ShimSetting": [622, -7223, -8803, 712, 68, 4, 34, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From d24955042df899fdff1fc66ff6bf40ddf3269e5e Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:06:09 -0400 Subject: [PATCH 287/463] fill IntendedFor --- ...6_ses-003_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...6_ses-003_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...6_ses-003_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...6_ses-003_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...6_ses-003_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_epi.json b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_epi.json index dc3153364..f52fe7b7d 100644 --- a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998388, - -0.055579, - 0.0114739, - 0.056343, - 0.946541, - -0.317624 - ], + "ImageOrientationPatientDICOM": [0.998388, -0.055579, 0.0114739, 0.056343, 0.946541, -0.317624], "ImageOrientationText": "Tra>Cor(-18.5)>Sag(-0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-06_ses-003_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-003/func/sub-06_ses-003_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-003/func/sub-06_ses-003_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-003/func/sub-06_ses-003_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 629, - -7278, - -8798, - 571, - 1, - -235, - -32, - -8 - ], + "ShimSetting": [629, -7278, -8798, 571, 1, -235, -32, -8], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_epi.json b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_epi.json index 2b8f927b4..1d8601aae 100644 --- a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998388, - -0.055579, - 0.0114739, - 0.056343, - 0.946541, - -0.317624 - ], + "ImageOrientationPatientDICOM": [0.998388, -0.055579, 0.0114739, 0.056343, 0.946541, -0.317624], "ImageOrientationText": "Tra>Cor(-18.5)>Sag(-0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-06_ses-003_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 629, - -7278, - -8798, - 571, - 1, - -235, - -32, - -8 - ], + "ShimSetting": [629, -7278, -8798, 571, 1, -235, -32, -8], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_epi.json b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_epi.json index 10ff4c964..67852296d 100644 --- a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998388, - -0.055579, - 0.0114739, - 0.056343, - 0.946541, - -0.317624 - ], + "ImageOrientationPatientDICOM": [0.998388, -0.055579, 0.0114739, 0.056343, 0.946541, -0.317624], "ImageOrientationText": "Tra>Cor(-18.5)>Sag(-0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-06_ses-003_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 629, - -7278, - -8798, - 571, - 1, - -235, - -32, - -8 - ], + "ShimSetting": [629, -7278, -8798, 571, 1, -235, -32, -8], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_epi.json b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_epi.json index 03a183159..bb82f2d2c 100644 --- a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998388, - -0.055579, - 0.0114739, - 0.056343, - 0.946541, - -0.317624 - ], + "ImageOrientationPatientDICOM": [0.998388, -0.055579, 0.0114739, 0.056343, 0.946541, -0.317624], "ImageOrientationText": "Tra>Cor(-18.5)>Sag(-0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-06_ses-003_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 629, - -7278, - -8798, - 571, - 1, - -235, - -32, - -8 - ], + "ShimSetting": [629, -7278, -8798, 571, 1, -235, -32, -8], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_epi.json b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_epi.json index 369170fee..98e3a5216 100644 --- a/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-06/ses-003/fmap/sub-06_ses-003_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998388, - -0.055579, - 0.0114739, - 0.056343, - 0.946541, - -0.317624 - ], + "ImageOrientationPatientDICOM": [0.998388, -0.055579, 0.0114739, 0.056343, 0.946541, -0.317624], "ImageOrientationText": "Tra>Cor(-18.5)>Sag(-0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-06_ses-003_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 629, - -7278, - -8798, - 571, - 1, - -235, - -32, - -8 - ], + "ShimSetting": [629, -7278, -8798, 571, 1, -235, -32, -8], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 255d1c35aae76de01155397f3314939da131a5a4 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:06:10 -0400 Subject: [PATCH 288/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-019_acq-axial_localizer.json | 81 +++ .../sub-02_ses-019_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-019_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-019_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-019_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-019_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-019/anat/sub-02_ses-019_scout.json | 542 ++++++++++++++++++ .../ses-019/anat/sub-02_ses-019_scout.nii.gz | 1 + ...9_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-06_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-06_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 + ...-019_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...19_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...019_task-mario3_run-01_part-mag_events.tsv | 1 + ...019_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...19_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-01_part-phase_events.tsv | 1 + ...9_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-019_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...19_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...019_task-mario3_run-02_part-mag_events.tsv | 1 + ...019_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...19_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-02_part-phase_events.tsv | 1 + ...9_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-019_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...19_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...019_task-mario3_run-03_part-mag_events.tsv | 1 + ...019_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...19_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-03_part-phase_events.tsv | 1 + ...9_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-019_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...19_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...019_task-mario3_run-04_part-mag_events.tsv | 1 + ...019_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...19_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-04_part-phase_events.tsv | 1 + ...9_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-019_task-mario3_run-05_part-mag_bold.json | 172 ++++++ ...19_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...019_task-mario3_run-05_part-mag_events.tsv | 1 + ...019_task-mario3_run-05_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...19_task-mario3_run-05_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-05_part-phase_events.tsv | 1 + ...9_task-mario3_run-05_part-phase_sbref.json | 153 +++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + ...-019_task-mario3_run-06_part-mag_bold.json | 172 ++++++ ...19_task-mario3_run-06_part-mag_bold.nii.gz | 1 + ...019_task-mario3_run-06_part-mag_events.tsv | 1 + ...019_task-mario3_run-06_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-06_part-mag_sbref.nii.gz | 1 + ...19_task-mario3_run-06_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-06_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-06_part-phase_events.tsv | 1 + ...9_task-mario3_run-06_part-phase_sbref.json | 153 +++++ ...task-mario3_run-06_part-phase_sbref.nii.gz | 1 + sub-02/ses-019/sub-02_ses-019_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 107 files changed, 7333 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-019/anat/sub-02_ses-019_acq-axial_localizer.json create mode 120000 sub-02/ses-019/anat/sub-02_ses-019_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-019/anat/sub-02_ses-019_acq-coronal_localizer.json create mode 120000 sub-02/ses-019/anat/sub-02_ses-019_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-019/anat/sub-02_ses-019_acq-sagittal_localizer.json create mode 120000 sub-02/ses-019/anat/sub-02_ses-019_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-019/anat/sub-02_ses-019_scout.json create mode 120000 sub-02/ses-019/anat/sub-02_ses-019_scout.nii.gz create mode 100644 sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 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a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..5b4512be8 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 51 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-019/anat/sub-02_ses-019_acq-axial_localizer.json b/sub-02/ses-019/anat/sub-02_ses-019_acq-axial_localizer.json new file mode 100644 index 000000000..6a6a8fe2f --- /dev/null +++ b/sub-02/ses-019/anat/sub-02_ses-019_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:37:6.172500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + 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"SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 249.545 +} \ No newline at end of file diff --git a/sub-02/ses-019/anat/sub-02_ses-019_acq-axial_localizer.nii.gz b/sub-02/ses-019/anat/sub-02_ses-019_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..273bef5d1 --- /dev/null +++ b/sub-02/ses-019/anat/sub-02_ses-019_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/zm/1x/MD5E-s181727--8cdf8826ec91d9d3ccf7c4ea159bb03b.nii.gz/MD5E-s181727--8cdf8826ec91d9d3ccf7c4ea159bb03b.nii.gz \ No newline at end of file diff --git a/sub-02/ses-019/anat/sub-02_ses-019_acq-coronal_localizer.json b/sub-02/ses-019/anat/sub-02_ses-019_acq-coronal_localizer.json new file mode 100644 index 000000000..0c5437780 --- /dev/null +++ b/sub-02/ses-019/anat/sub-02_ses-019_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:37:13.162500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0279184, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 249.545 +} \ No newline at end of file diff --git a/sub-02/ses-019/anat/sub-02_ses-019_acq-coronal_localizer.nii.gz 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a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-phase_bold.nii.gz b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-phase_bold.nii.gz new file mode 120000 index 000000000..37e79e2ab --- /dev/null +++ b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-phase_bold.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/pP/04/MD5E-s348274995--f8e266eb6c825f24e205fae1584aa343.nii.gz/MD5E-s348274995--f8e266eb6c825f24e205fae1584aa343.nii.gz \ No newline at end of file diff --git a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-phase_events.tsv b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-phase_events.tsv new file mode 120000 index 000000000..1bbdfddb5 --- /dev/null +++ b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-phase_events.tsv @@ -0,0 +1 @@ +../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-phase_sbref.json b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-phase_sbref.json new file mode 100644 index 000000000..766b647d2 --- /dev/null +++ b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-phase_sbref.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:39:23.267500", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTime1": 0.037, + "EchoTime2": 0.001, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Single-band reference", + "ImageOrientationPatientDICOM": [ + 0.998349, + -0.00403019, + 0.0572932, + 0.0334675, + 0.851501, + -0.523283 + ], + "ImageOrientationText": "Tra>Cor(-31.7)>Sag(2.7)", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "P", + "ND", + "MOSAIC", + "PHASE" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": 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+ 4.705, + 4.8025, + 4.9, + 4.9975, + 5.095, + 5.195, + 5.2925, + 5.39, + 5.4875, + 5.585, + 5.685, + 5.7825 + ], + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 249.545, + "WipMemBlock": "7782a2a9-4474-4950-afe2-faf083bda33e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-phase_sbref.nii.gz b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-phase_sbref.nii.gz new file mode 120000 index 000000000..ef53897ba --- /dev/null +++ b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Qp/jF/MD5E-s1103322--6fe0243b4bae6424e89ec8e9aff0b93a.nii.gz/MD5E-s1103322--6fe0243b4bae6424e89ec8e9aff0b93a.nii.gz \ No newline at end of file diff --git a/sub-02/ses-019/sub-02_ses-019_scans.tsv b/sub-02/ses-019/sub-02_ses-019_scans.tsv new file mode 120000 index 000000000..3ff418a0f --- /dev/null +++ b/sub-02/ses-019/sub-02_ses-019_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/Kj/4w/MD5E-s4533--d0ed1cea277bb13bc3732377d5271b5b.tsv/MD5E-s4533--d0ed1cea277bb13bc3732377d5271b5b.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..1642fdea1 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.998349, -0.00403019, 0.0572932, 0.0334675, 0.851501, -0.523283], + "ImageOrientationText": "Tra>Cor(-31.7)>Sag(2.7)", + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0411211, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [616, -7179, -8853, 319, 10, -110, -53, 29], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 249.545, + "dcmmeta_affine": [ + [-1.9966984987258911, 0.06693509221076965, 0.09335267543792725, 101.9434814453125], + [0.008060373365879059, 1.703002691268921, -1.0486738681793213, -56.336402893066406], + [0.11458646506071091, 1.0465664863586426, 1.7004612684249878, -99.49699401855469], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 208538a7896f0adb3c9b58b88fd5ecc647de0560 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:06:19 -0400 Subject: [PATCH 289/463] fill IntendedFor --- ...6_ses-005_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...6_ses-005_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...6_ses-005_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...6_ses-005_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_epi.json b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_epi.json index b50dbaf3b..bdab2a24c 100644 --- a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999287, - -0.0377577, - 0.000458971, - 0.035769, - 0.942619, - -0.331948 - ], + "ImageOrientationPatientDICOM": [0.999287, -0.0377577, 0.000458971, 0.035769, 0.942619, -0.331948], "ImageOrientationText": "Tra>Cor(-19.4)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-06_ses-005_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-005/func/sub-06_ses-005_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-005/func/sub-06_ses-005_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 618, - -7254, - -8843, - 562, - 8, - -232, - -47, - -34 - ], + "ShimSetting": [618, -7254, -8843, 562, 8, -232, -47, -34], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_epi.json b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_epi.json index f970ee5ad..38bc20176 100644 --- a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999287, - -0.0377577, - 0.000458971, - 0.035769, - 0.942619, - -0.331948 - ], + "ImageOrientationPatientDICOM": [0.999287, -0.0377577, 0.000458971, 0.035769, 0.942619, -0.331948], "ImageOrientationText": "Tra>Cor(-19.4)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-06_ses-005_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 618, - -7254, - -8843, - 562, - 8, - -232, - -47, - -34 - ], + "ShimSetting": [618, -7254, -8843, 562, 8, -232, -47, -34], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_epi.json b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_epi.json index b6b193e67..56f7f10ff 100644 --- a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999287, - -0.0377577, - 0.000458971, - 0.035769, - 0.942619, - -0.331948 - ], + "ImageOrientationPatientDICOM": [0.999287, -0.0377577, 0.000458971, 0.035769, 0.942619, -0.331948], "ImageOrientationText": "Tra>Cor(-19.4)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-06_ses-005_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 618, - -7254, - -8843, - 562, - 8, - -232, - -47, - -34 - ], + "ShimSetting": [618, -7254, -8843, 562, 8, -232, -47, -34], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_epi.json b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_epi.json index 8eb6e4bd5..d81b4795f 100644 --- a/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-06/ses-005/fmap/sub-06_ses-005_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999287, - -0.0377577, - 0.000458971, - 0.035769, - 0.942619, - -0.331948 - ], + "ImageOrientationPatientDICOM": [0.999287, -0.0377577, 0.000458971, 0.035769, 0.942619, -0.331948], "ImageOrientationText": "Tra>Cor(-19.4)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-005/func/sub-06_ses-005_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 618, - -7254, - -8843, - 562, - 8, - -232, - -47, - -34 - ], + "ShimSetting": [618, -7254, -8843, 562, 8, -232, -47, -34], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 667619480ce4faef7e4556a69504862aced5ca25 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:07:27 -0400 Subject: [PATCH 290/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..d02fb960b --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 9dd6252b-b6ee-4337-a714-1f7a0c374bdb diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..9f425c43f --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 9f425c43f94f6022f16e999220931f47e17a0d38 From bf99b43c0d715d918eefed6e0a6f795678b6af05 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:07:59 -0400 Subject: [PATCH 291/463] fix fmap phase --- ...2_ses-019_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-019_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-019_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-019_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-019_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-019_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-019_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-019_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-019_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-019_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-019_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-019_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-019_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-019_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - ..._ses-019_acq-sbref_dir-PA_run-06_epi.json} | 0 ...es-019_acq-sbref_dir-PA_run-06_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 - sub-02/ses-019/sub-02_ses-019_scans.tsv | 2 +- 33 files changed, 1 insertion(+), 1250 deletions(-) rename sub-02/ses-019/fmap/{sub-02_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-019_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-019/fmap/{sub-02_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-019_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-019/fmap/{sub-02_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-019_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-019/fmap/{sub-02_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-019_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-019/fmap/{sub-02_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-019_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-019/fmap/{sub-02_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-019_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-019/fmap/{sub-02_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-019_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-019/fmap/{sub-02_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-019_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-019/fmap/{sub-02_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-019_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-019/fmap/{sub-02_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-019_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-02/ses-019/fmap/{sub-02_ses-019_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-02_ses-019_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-02/ses-019/fmap/{sub-02_ses-019_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-02_ses-019_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-02/ses-019/fmap/{sub-02_ses-019_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-02_ses-019_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-02/ses-019/fmap/{sub-02_ses-019_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-02_ses-019_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz rename sub-02/ses-019/fmap/{sub-02_ses-019_acq-sbref_dir-PA_run-06_part-mag_epi.json => sub-02_ses-019_acq-sbref_dir-PA_run-06_epi.json} (100%) rename sub-02/ses-019/fmap/{sub-02_ses-019_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz => sub-02_ses-019_acq-sbref_dir-PA_run-06_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_part-phase_epi.json delete mode 120000 sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index cbdcf17d8..000000000 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:39:9.380000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": 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2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.0327942453661, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "153956.337000", - "SliceLocation": -50.297791269217, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000251602, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "151822.692000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["153909.380000", "153910.870000", "153912.360000"], - "ContentTime": ["153956.339000", "153956.342000", "153956.344000"], - "InstanceCreationTime": ["153956.339000", "153956.342000", "153956.344000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4914.0, 4882.0, 4912.0], - "WindowWidth": [18768.0, 18736.0, 18764.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 6dad238eb..000000000 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/ww/Zz/MD5E-s3332786--a8bb1736b3ad3e82f93796bb40997b38.nii.gz/MD5E-s3332786--a8bb1736b3ad3e82f93796bb40997b38.nii.gz \ No newline at end of file diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 3577db3d0..000000000 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:38:58.950000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998349, - -0.00403019, - 0.0572932, - 0.0334675, - 0.851501, - -0.523283 - ], - "ImageOrientationText": "Tra>Cor(-31.7)>Sag(2.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0327942, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 616, - -7179, - -8853, - 319, - 10, - -110, - -53, - 29 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 249.545, - "WipMemBlock": "ad9d61bd-099d-4bef-844f-6ec9dc09a7e3||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 7e68adf10..000000000 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/pm/3q/MD5E-s1112033--db377bffbab28c83417544c755a1df8e.nii.gz/MD5E-s1112033--db377bffbab28c83417544c755a1df8e.nii.gz \ No newline at end of file diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index c2347a1e2..000000000 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:40:42.995000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998349, - -0.00403019, - 0.0572932, - 0.0334675, - 0.851501, - -0.523283 - ], - "ImageOrientationText": "Tra>Cor(-31.7)>Sag(2.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0411211, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 616, - -7179, - -8853, - 319, - 10, - -110, - -53, - 29 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 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a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3V/g8/MD5E-s1103126--775a505739a3cef34cbde0c4c76abe80.nii.gz/MD5E-s1103126--775a505739a3cef34cbde0c4c76abe80.nii.gz \ No newline at end of file diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 8f2163f4f..000000000 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:58:48.720000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": 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"ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0411211, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 616, - -7179, - -8853, - 319, - 10, - -110, - -53, - 29 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 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a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index c61abfbd6..000000000 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:09:16.730000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998349, - -0.00403019, - 0.0572932, - 0.0334675, - 0.851501, - -0.523283 - ], - "ImageOrientationText": 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"RepetitionTime": 1.49, - "SAR": 0.0411211, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 616, - -7179, - -8853, - 319, - 10, - -110, - -53, - 29 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": 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sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 04dc6805f..000000000 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:18:12.855000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998349, - -0.00403019, - 0.0572932, - 0.0334675, - 0.851501, - -0.523283 - ], - "ImageOrientationText": "Tra>Cor(-31.7)>Sag(2.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0411211, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 616, - -7179, 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a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 5199d44f8..000000000 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/7P/7w/MD5E-s1103156--80e94c9daa4af6d75486d240e299115d.nii.gz/MD5E-s1103156--80e94c9daa4af6d75486d240e299115d.nii.gz \ No newline at end of file diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index 5bb84e0bf..000000000 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:28:54.260000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998349, - -0.00403019, - 0.0572932, - 0.0334675, - 0.851501, - -0.523283 - ], - "ImageOrientationText": "Tra>Cor(-31.7)>Sag(2.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-05", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0411211, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 616, - -7179, - -8853, - 319, - 10, - -110, - -53, - 29 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 249.545, - "WipMemBlock": "4ed3da87-06da-491e-85ab-f42f00c54a10||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index 24f683f60..000000000 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/4M/0V/MD5E-s1103284--0b77549f6fdb31259ec4957bd0b2f572.nii.gz/MD5E-s1103284--0b77549f6fdb31259ec4957bd0b2f572.nii.gz \ No newline at end of file diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_part-mag_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_epi.json similarity index 100% rename from sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_part-mag_epi.json rename to sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_epi.json diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_epi.nii.gz similarity index 100% rename from sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz rename to sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_epi.nii.gz diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_part-phase_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_part-phase_epi.json deleted file mode 100644 index 607fc4190..000000000 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:39:23.267500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998349, - -0.00403019, - 0.0572932, - 0.0334675, - 0.851501, - -0.523283 - ], - "ImageOrientationText": "Tra>Cor(-31.7)>Sag(2.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-06", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0411211, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-06_SBRef", - "SeriesNumber": 24, - "ShimSetting": [ - 616, - -7179, - -8853, - 319, - 10, - -110, - -53, - 29 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 249.545, - "WipMemBlock": "7782a2a9-4474-4950-afe2-faf083bda33e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz deleted file mode 120000 index ef53897ba..000000000 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Qp/jF/MD5E-s1103322--6fe0243b4bae6424e89ec8e9aff0b93a.nii.gz/MD5E-s1103322--6fe0243b4bae6424e89ec8e9aff0b93a.nii.gz \ No newline at end of file diff --git a/sub-02/ses-019/sub-02_ses-019_scans.tsv b/sub-02/ses-019/sub-02_ses-019_scans.tsv index 3ff418a0f..6fca08505 120000 --- a/sub-02/ses-019/sub-02_ses-019_scans.tsv +++ b/sub-02/ses-019/sub-02_ses-019_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/Kj/4w/MD5E-s4533--d0ed1cea277bb13bc3732377d5271b5b.tsv/MD5E-s4533--d0ed1cea277bb13bc3732377d5271b5b.tsv \ No newline at end of file +../../.git/annex/objects/w5/Wz/MD5E-s3569--6bf1611df6e64c7d948ac1f8261cda33.tsv/MD5E-s3569--6bf1611df6e64c7d948ac1f8261cda33.tsv \ No newline at end of file From f6fc43aac940842f118e1c2aa9fb1f18b37d8d5b Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:08:20 -0400 Subject: [PATCH 292/463] fix complex event files --- ...g_events.tsv => sub-02_ses-019_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-02_ses-019_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-02_ses-019_task-mario3_run-03_events.tsv} | 0 ...e_events.tsv => sub-02_ses-019_task-mario3_run-04_events.tsv} | 0 .../func/sub-02_ses-019_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-02_ses-019_task-mario3_run-04_part-phase_events.tsv | 1 - ...g_events.tsv => sub-02_ses-019_task-mario3_run-05_events.tsv} | 0 .../func/sub-02_ses-019_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-02_ses-019_task-mario3_run-05_part-phase_events.tsv | 1 - ...e_events.tsv => sub-02_ses-019_task-mario3_run-06_events.tsv} | 0 .../func/sub-02_ses-019_task-mario3_run-06_part-mag_events.tsv | 1 - .../func/sub-02_ses-019_task-mario3_run-06_part-phase_events.tsv | 1 - 12 files changed, 6 deletions(-) rename sub-02/ses-019/func/{sub-02_ses-019_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-019_task-mario3_run-01_events.tsv} (100%) rename sub-02/ses-019/func/{sub-02_ses-019_task-mario3_run-01_part-phase_events.tsv => sub-02_ses-019_task-mario3_run-02_events.tsv} (100%) rename sub-02/ses-019/func/{sub-02_ses-019_task-mario3_run-02_part-mag_events.tsv => sub-02_ses-019_task-mario3_run-03_events.tsv} (100%) rename sub-02/ses-019/func/{sub-02_ses-019_task-mario3_run-02_part-phase_events.tsv => sub-02_ses-019_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-04_part-phase_events.tsv rename sub-02/ses-019/func/{sub-02_ses-019_task-mario3_run-03_part-mag_events.tsv => sub-02_ses-019_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-05_part-phase_events.tsv rename sub-02/ses-019/func/{sub-02_ses-019_task-mario3_run-03_part-phase_events.tsv => sub-02_ses-019_task-mario3_run-06_events.tsv} (100%) delete mode 120000 sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-mag_events.tsv delete mode 120000 sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-phase_events.tsv diff --git a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-02_events.tsv similarity index 100% rename from sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-01_part-phase_events.tsv rename to sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-02_events.tsv diff --git a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-02_part-mag_events.tsv b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-03_events.tsv similarity index 100% rename from sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-02_part-mag_events.tsv rename to sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-03_events.tsv diff --git a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-02_part-phase_events.tsv b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-04_events.tsv similarity index 100% rename from sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-02_part-phase_events.tsv rename to sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-04_events.tsv diff --git a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-04_part-mag_events.tsv b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-04_part-phase_events.tsv b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-03_part-mag_events.tsv b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-05_events.tsv similarity index 100% rename from sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-03_part-mag_events.tsv rename to sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-05_events.tsv diff --git a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-05_part-mag_events.tsv b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-05_part-phase_events.tsv b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_events.tsv similarity index 100% rename from sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-03_part-phase_events.tsv rename to sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_events.tsv diff --git a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-mag_events.tsv b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-phase_events.tsv b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 9e9ad96bf15667f4c189cfcabf142bfc45bfc7a4 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:08:24 -0400 Subject: [PATCH 293/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-06_ses-008_acq-axial_localizer.json | 81 +++ .../sub-06_ses-008_acq-axial_localizer.nii.gz | 1 + .../sub-06_ses-008_acq-coronal_localizer.json | 81 +++ ...ub-06_ses-008_acq-coronal_localizer.nii.gz | 1 + ...sub-06_ses-008_acq-sagittal_localizer.json | 86 +++ ...b-06_ses-008_acq-sagittal_localizer.nii.gz | 1 + sub-06/ses-008/anat/sub-06_ses-008_scout.json | 542 ++++++++++++++++++ .../ses-008/anat/sub-06_ses-008_scout.nii.gz | 1 + ...8_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-008_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-01_part-mag_events.tsv | 1 + ...008_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-01_part-phase_events.tsv | 1 + ...8_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-008_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-02_part-mag_events.tsv | 1 + ...008_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-02_part-phase_events.tsv | 1 + ...8_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-008_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-03_part-mag_events.tsv | 1 + ...008_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-03_part-phase_events.tsv | 1 + ...8_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-06/ses-008/sub-06_ses-008_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-06/ses-008/anat/sub-06_ses-008_acq-axial_localizer.json create mode 120000 sub-06/ses-008/anat/sub-06_ses-008_acq-axial_localizer.nii.gz create mode 100644 sub-06/ses-008/anat/sub-06_ses-008_acq-coronal_localizer.json create mode 120000 sub-06/ses-008/anat/sub-06_ses-008_acq-coronal_localizer.nii.gz create mode 100644 sub-06/ses-008/anat/sub-06_ses-008_acq-sagittal_localizer.json create mode 120000 sub-06/ses-008/anat/sub-06_ses-008_acq-sagittal_localizer.nii.gz create mode 100644 sub-06/ses-008/anat/sub-06_ses-008_scout.json create mode 120000 sub-06/ses-008/anat/sub-06_ses-008_scout.nii.gz create mode 100644 sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-06/ses-008/sub-06_ses-008_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 9f425c43f..515f85f09 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 9f425c43f94f6022f16e999220931f47e17a0d38 +Subproject commit 515f85f091c35cf613c6ca9e45126f82fdf1203e diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..db37a3f34 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-06 41 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-06/ses-008/anat/sub-06_ses-008_acq-axial_localizer.json b/sub-06/ses-008/anat/sub-06_ses-008_acq-axial_localizer.json new file mode 100644 index 000000000..d458bbe80 --- /dev/null +++ b/sub-06/ses-008/anat/sub-06_ses-008_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:28:0.065000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0545669, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 288.737 +} \ No newline at end of file diff --git a/sub-06/ses-008/anat/sub-06_ses-008_acq-axial_localizer.nii.gz b/sub-06/ses-008/anat/sub-06_ses-008_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..bcdb0ae90 --- /dev/null +++ b/sub-06/ses-008/anat/sub-06_ses-008_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Vp/f9/MD5E-s163796--48e57509cb9f6928eae7c44796b7b248.nii.gz/MD5E-s163796--48e57509cb9f6928eae7c44796b7b248.nii.gz \ No newline at end of file diff --git a/sub-06/ses-008/anat/sub-06_ses-008_acq-coronal_localizer.json b/sub-06/ses-008/anat/sub-06_ses-008_acq-coronal_localizer.json new file mode 100644 index 000000000..5f425443c --- /dev/null +++ b/sub-06/ses-008/anat/sub-06_ses-008_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:28:7.055000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": 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+../../.git/annex/objects/89/zg/MD5E-s2667--69329946b95b92c304a023a17ce3d7df.tsv/MD5E-s2667--69329946b95b92c304a023a17ce3d7df.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..3c908f7b0 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": 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"ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0803716, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [620, -7239, -8861, 490, 30, -273, -140, 7], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 288.737, + "dcmmeta_affine": [ + [-1.9996110200881958, 0.012563979253172874, -0.03738714009523392, 106.74517059326172], + [0.026528725400567055, 1.8313332796096802, -0.8034393787384033, -61.24659729003906], + [-0.029186958447098732, 0.8037790060043335, 1.8311437368392944, -76.48253631591797], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From d757d09c928ac9598c9fab85d16667d1cc4fe06b Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:09:25 -0400 Subject: [PATCH 294/463] fix fmap phase --- ...6_ses-008_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-008_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-008_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-06/ses-008/sub-06_ses-008_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-06/ses-008/fmap/{sub-06_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-06_ses-008_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-008/fmap/{sub-06_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-008_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-008/fmap/{sub-06_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-06_ses-008_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-008/fmap/{sub-06_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-008_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-008/fmap/{sub-06_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-06_ses-008_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-06/ses-008/fmap/{sub-06_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-06_ses-008_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-06/ses-008/fmap/{sub-06_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-06_ses-008_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-06/ses-008/fmap/{sub-06_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-06_ses-008_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-06/ses-008/fmap/{sub-06_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-06_ses-008_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-06/ses-008/fmap/{sub-06_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-06_ses-008_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index a3f7eba66..000000000 --- a/sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:29:2.260000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999806, -0.0132644, -0.0145935, 0.00628199, 0.915667, -0.40189], - "ImageOrientationText": "Tra>Cor(-23.7)>Sag(-1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0640967, - "ScanOptions": "FS", - "ScanningSequence": 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a/sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index d5e37cefc..000000000 --- a/sub-06/ses-008/fmap/sub-06_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/q8/KZ/MD5E-s3335078--af1b4d6ea54d5c68a39de1fc0d7f5d16.nii.gz/MD5E-s3335078--af1b4d6ea54d5c68a39de1fc0d7f5d16.nii.gz \ No newline at end of file diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 1f6c2d351..000000000 --- a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:28:51.830000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - 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a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/xw/0Z/MD5E-s1112521--6b3b6892a747f72a33457393faa51208.nii.gz/MD5E-s1112521--6b3b6892a747f72a33457393faa51208.nii.gz \ No newline at end of file diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index dcb8c2c4e..000000000 --- a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:30:1.667500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": 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- "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0803716, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 620, - -7239, - -8861, - 490, - 30, - -273, - -140, - 7 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 288.737, - "WipMemBlock": "57a3d08d-0bf2-4407-91b3-1154ec9120cd||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 6531816d7..000000000 --- a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/gG/5w/MD5E-s1103474--462f0649cc4c343f6a45919d9a703f40.nii.gz/MD5E-s1103474--462f0649cc4c343f6a45919d9a703f40.nii.gz \ No newline at end of file diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 9002d0335..000000000 --- a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:39:51.130000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999806, - -0.0132644, - -0.0145935, - 0.00628199, - 0.915667, - -0.40189 - ], - "ImageOrientationText": 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"RepetitionTime": 1.49, - "SAR": 0.0803716, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 620, - -7239, - -8861, - 490, - 30, - -273, - -140, - 7 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 288.737, - "WipMemBlock": "693b4dfd-435f-45c9-8c3d-0106bffcc8c2||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 8a4ece4c2..000000000 --- a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/j8/pw/MD5E-s1103639--3d0be932146cc2a1b82fdf3c8ca7f8ea.nii.gz/MD5E-s1103639--3d0be932146cc2a1b82fdf3c8ca7f8ea.nii.gz \ No newline at end of file diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index a838c0d16..000000000 --- a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:49:6.152500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999806, - -0.0132644, - -0.0145935, - 0.00628199, - 0.915667, - -0.40189 - ], - "ImageOrientationText": "Tra>Cor(-23.7)>Sag(-1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0803716, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 620, - -7239, - -8861, - 490, - 30, - -273, - -140, - 7 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 288.737, - "WipMemBlock": "f7e27323-8fd4-43c2-8805-710abb39ee40||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index e4d6c08b4..000000000 --- a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/gM/f9/MD5E-s1103719--64fe9ab95dc1411dbda723055f77c004.nii.gz/MD5E-s1103719--64fe9ab95dc1411dbda723055f77c004.nii.gz \ No newline at end of file diff --git a/sub-06/ses-008/sub-06_ses-008_scans.tsv b/sub-06/ses-008/sub-06_ses-008_scans.tsv index 6d20c6e35..0e3198ca5 120000 --- a/sub-06/ses-008/sub-06_ses-008_scans.tsv +++ b/sub-06/ses-008/sub-06_ses-008_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/89/zg/MD5E-s2667--69329946b95b92c304a023a17ce3d7df.tsv/MD5E-s2667--69329946b95b92c304a023a17ce3d7df.tsv \ No newline at end of file +../../.git/annex/objects/g0/Mg/MD5E-s2066--f39062a41b67df39756b1d7972b8fae5.tsv/MD5E-s2066--f39062a41b67df39756b1d7972b8fae5.tsv \ No newline at end of file From 3a784f646973e8095be71f418a1ea91633fd11f4 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:09:33 -0400 Subject: [PATCH 295/463] fill IntendedFor --- ...2_ses-019_acq-sbref_dir-AP_run-01_epi.json | 93 +++---------------- ...2_ses-019_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...2_ses-019_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...2_ses-019_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...2_ses-019_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- ...2_ses-019_acq-sbref_dir-PA_run-05_epi.json | 88 ++---------------- ...2_ses-019_acq-sbref_dir-PA_run-06_epi.json | 88 ++---------------- 7 files changed, 54 insertions(+), 567 deletions(-) diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_epi.json index 56a0a80c3..bd75c9fde 100644 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998349, - -0.00403019, - 0.0572932, - 0.0334675, - 0.851501, - -0.523283 - ], + "ImageOrientationPatientDICOM": [0.998349, -0.00403019, 0.0572932, 0.0334675, 0.851501, -0.523283], "ImageOrientationText": "Tra>Cor(-31.7)>Sag(2.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,20 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-019/func/sub-02_ses-019_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-019/func/sub-02_ses-019_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-019/func/sub-02_ses-019_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-019/func/sub-02_ses-019_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-019/func/sub-02_ses-019_task-mario3_run-05_part-mag_bold.nii.gz", + "ses-019/func/sub-02_ses-019_task-mario3_run-06_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +68,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 616, - -7179, - -8853, - 319, - 10, - -110, - -53, - 29 - ], + "ShimSetting": [616, -7179, -8853, 319, 10, -110, -53, 29], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_epi.json index dac8c6cac..556a7a7fb 100644 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998349, - -0.00403019, - 0.0572932, - 0.0334675, - 0.851501, - -0.523283 - ], + "ImageOrientationPatientDICOM": [0.998349, -0.00403019, 0.0572932, 0.0334675, 0.851501, -0.523283], "ImageOrientationText": "Tra>Cor(-31.7)>Sag(2.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-019/func/sub-02_ses-019_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 616, - -7179, - -8853, - 319, - 10, - -110, - -53, - 29 - ], + "ShimSetting": [616, -7179, -8853, 319, 10, -110, -53, 29], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_epi.json index 563dbd0d6..6ab9d2229 100644 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998349, - -0.00403019, - 0.0572932, - 0.0334675, - 0.851501, - -0.523283 - ], + "ImageOrientationPatientDICOM": [0.998349, -0.00403019, 0.0572932, 0.0334675, 0.851501, -0.523283], "ImageOrientationText": "Tra>Cor(-31.7)>Sag(2.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-019/func/sub-02_ses-019_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 616, - -7179, - -8853, - 319, - 10, - -110, - -53, - 29 - ], + "ShimSetting": [616, -7179, -8853, 319, 10, -110, -53, 29], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-03_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-03_epi.json index 1efcfff82..83f6749fd 100644 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998349, - -0.00403019, - 0.0572932, - 0.0334675, - 0.851501, - -0.523283 - ], + "ImageOrientationPatientDICOM": [0.998349, -0.00403019, 0.0572932, 0.0334675, 0.851501, -0.523283], "ImageOrientationText": "Tra>Cor(-31.7)>Sag(2.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-019/func/sub-02_ses-019_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 616, - -7179, - -8853, - 319, - 10, - -110, - -53, - 29 - ], + "ShimSetting": [616, -7179, -8853, 319, 10, -110, -53, 29], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-04_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-04_epi.json index c2296a211..85b2be966 100644 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998349, - -0.00403019, - 0.0572932, - 0.0334675, - 0.851501, - -0.523283 - ], + "ImageOrientationPatientDICOM": [0.998349, -0.00403019, 0.0572932, 0.0334675, 0.851501, -0.523283], "ImageOrientationText": "Tra>Cor(-31.7)>Sag(2.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-019/func/sub-02_ses-019_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 616, - -7179, - -8853, - 319, - 10, - -110, - -53, - 29 - ], + "ShimSetting": [616, -7179, -8853, 319, 10, -110, -53, 29], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_epi.json index 923d3b080..53228f11c 100644 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998349, - -0.00403019, - 0.0572932, - 0.0334675, - 0.851501, - -0.523283 - ], + "ImageOrientationPatientDICOM": [0.998349, -0.00403019, 0.0572932, 0.0334675, 0.851501, -0.523283], "ImageOrientationText": "Tra>Cor(-31.7)>Sag(2.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-019/func/sub-02_ses-019_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 616, - -7179, - -8853, - 319, - 10, - -110, - -53, - 29 - ], + "ShimSetting": [616, -7179, -8853, 319, 10, -110, -53, 29], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_epi.json b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_epi.json index a8d0fc38c..17e4ba279 100644 --- a/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_epi.json +++ b/sub-02/ses-019/fmap/sub-02_ses-019_acq-sbref_dir-PA_run-06_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998349, - -0.00403019, - 0.0572932, - 0.0334675, - 0.851501, - -0.523283 - ], + "ImageOrientationPatientDICOM": [0.998349, -0.00403019, 0.0572932, 0.0334675, 0.851501, -0.523283], "ImageOrientationText": "Tra>Cor(-31.7)>Sag(2.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-019/func/sub-02_ses-019_task-mario3_run-06_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-06_SBRef", "SeriesNumber": 24, - "ShimSetting": [ - 616, - -7179, - -8853, - 319, - 10, - -110, - -53, - 29 - ], + "ShimSetting": [616, -7179, -8853, 319, 10, -110, -53, 29], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From e23a9536afab881465843237efc6741fd5b6914f Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:09:43 -0400 Subject: [PATCH 296/463] fix complex event files --- ...g_events.tsv => sub-06_ses-008_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-06_ses-008_task-mario3_run-02_events.tsv} | 0 .../func/sub-06_ses-008_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-06_ses-008_task-mario3_run-03_events.tsv} | 0 .../func/sub-06_ses-008_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-06_ses-008_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-06/ses-008/func/{sub-06_ses-008_task-mario3_run-01_part-mag_events.tsv => sub-06_ses-008_task-mario3_run-01_events.tsv} (100%) rename sub-06/ses-008/func/{sub-06_ses-008_task-mario3_run-01_part-phase_events.tsv => sub-06_ses-008_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-02_part-phase_events.tsv rename sub-06/ses-008/func/{sub-06_ses-008_task-mario3_run-02_part-mag_events.tsv => sub-06_ses-008_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-01_part-mag_events.tsv b/sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-01_events.tsv similarity index 100% rename from sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-01_part-mag_events.tsv rename to sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-01_events.tsv diff --git a/sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-01_part-phase_events.tsv b/sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-02_events.tsv similarity index 100% rename from sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-01_part-phase_events.tsv rename to sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-02_events.tsv diff --git a/sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-02_part-phase_events.tsv b/sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-02_part-mag_events.tsv b/sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_events.tsv similarity index 100% rename from sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-02_part-mag_events.tsv rename to sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_events.tsv diff --git a/sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_part-mag_events.tsv b/sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_part-phase_events.tsv b/sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-008/func/sub-06_ses-008_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From b66491cf5a7044ad05ea251850695b918177415a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:11:05 -0400 Subject: [PATCH 297/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..9ad54562b --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = ee9abb6f-a96b-4620-b782-06b82f3699c0 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..f9a1a53d1 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit f9a1a53d1406ebae682fc2c3018a630fd391c75d From e42549fd5165553ff88205747008a044fc54ea95 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:11:34 -0400 Subject: [PATCH 298/463] fill IntendedFor --- ...6_ses-008_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...6_ses-008_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...6_ses-008_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...6_ses-008_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_epi.json b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_epi.json index 16c8a5b3d..e98b7fc4f 100644 --- a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999806, - -0.0132644, - -0.0145935, - 0.00628199, - 0.915667, - -0.40189 - ], + "ImageOrientationPatientDICOM": [0.999806, -0.0132644, -0.0145935, 0.00628199, 0.915667, -0.40189], "ImageOrientationText": "Tra>Cor(-23.7)>Sag(-1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-06_ses-008_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-008/func/sub-06_ses-008_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-008/func/sub-06_ses-008_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 620, - -7239, - -8861, - 490, - 30, - -273, - -140, - 7 - ], + "ShimSetting": [620, -7239, -8861, 490, 30, -273, -140, 7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_epi.json b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_epi.json index 6ae907a3e..312c853f1 100644 --- a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999806, - -0.0132644, - -0.0145935, - 0.00628199, - 0.915667, - -0.40189 - ], + "ImageOrientationPatientDICOM": [0.999806, -0.0132644, -0.0145935, 0.00628199, 0.915667, -0.40189], "ImageOrientationText": "Tra>Cor(-23.7)>Sag(-1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-06_ses-008_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 620, - -7239, - -8861, - 490, - 30, - -273, - -140, - 7 - ], + "ShimSetting": [620, -7239, -8861, 490, 30, -273, -140, 7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_epi.json b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_epi.json index e6f3ea4ca..6707cef29 100644 --- a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999806, - -0.0132644, - -0.0145935, - 0.00628199, - 0.915667, - -0.40189 - ], + "ImageOrientationPatientDICOM": [0.999806, -0.0132644, -0.0145935, 0.00628199, 0.915667, -0.40189], "ImageOrientationText": "Tra>Cor(-23.7)>Sag(-1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-06_ses-008_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 620, - -7239, - -8861, - 490, - 30, - -273, - -140, - 7 - ], + "ShimSetting": [620, -7239, -8861, 490, 30, -273, -140, 7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_epi.json b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_epi.json index d525cc246..26202762b 100644 --- a/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-06/ses-008/fmap/sub-06_ses-008_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999806, - -0.0132644, - -0.0145935, - 0.00628199, - 0.915667, - -0.40189 - ], + "ImageOrientationPatientDICOM": [0.999806, -0.0132644, -0.0145935, 0.00628199, 0.915667, -0.40189], "ImageOrientationText": "Tra>Cor(-23.7)>Sag(-1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-06_ses-008_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 620, - -7239, - -8861, - 490, - 30, - -273, - -140, - 7 - ], + "ShimSetting": [620, -7239, -8861, 490, 30, -273, -140, 7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 17c9ed8a2fec1c9f323bab901a53e41bee81b86d Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:15:52 -0400 Subject: [PATCH 299/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..46ed00773 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = e8b16db4-82f4-4205-8498-c41963fbb03d diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..f7648a290 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit f7648a2907eb0e2eafe6bb1b42554bb186c2cd04 From ef72c588c79b394a4c0bdf588714d4e9ad0c4afb Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:15:59 -0400 Subject: [PATCH 300/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..23c11956b --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 0607eab9-39bb-4ba6-b4e6-f8d08907640d diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..02c6cd092 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 02c6cd09237a3cd8c72bc260cb6a1bb9ad734e10 From 746684f07681a0d6519031c9ed04453e0b3372ae Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:16:05 -0400 Subject: [PATCH 301/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..440e5634a --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 68738007-ff9b-4bfe-b8d6-1f9dc946321f diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..cc4a2d205 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit cc4a2d205f67c75ce6cef8e471846dcd8031efd4 From b15d61d2ebc0485a02d1b684d7fbe521fbabb60a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:16:37 -0400 Subject: [PATCH 302/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-06_ses-010_acq-axial_localizer.json | 81 +++ .../sub-06_ses-010_acq-axial_localizer.nii.gz | 1 + .../sub-06_ses-010_acq-coronal_localizer.json | 81 +++ ...ub-06_ses-010_acq-coronal_localizer.nii.gz | 1 + ...sub-06_ses-010_acq-sagittal_localizer.json | 86 +++ ...b-06_ses-010_acq-sagittal_localizer.nii.gz | 1 + sub-06/ses-010/anat/sub-06_ses-010_scout.json | 542 ++++++++++++++++++ .../ses-010/anat/sub-06_ses-010_scout.nii.gz | 1 + ...0_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-010_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...10_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...010_task-mario3_run-01_part-mag_events.tsv | 1 + ...010_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...0_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...10_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...0_task-mario3_run-01_part-phase_events.tsv | 1 + ...0_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-010_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...10_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...010_task-mario3_run-02_part-mag_events.tsv | 1 + ...010_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...0_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...10_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...0_task-mario3_run-02_part-phase_events.tsv | 1 + ...0_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-010_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...10_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...010_task-mario3_run-03_part-mag_events.tsv | 1 + ...010_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...0_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...10_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...0_task-mario3_run-03_part-phase_events.tsv | 1 + ...0_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-06/ses-010/sub-06_ses-010_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-06/ses-010/anat/sub-06_ses-010_acq-axial_localizer.json create mode 120000 sub-06/ses-010/anat/sub-06_ses-010_acq-axial_localizer.nii.gz create mode 100644 sub-06/ses-010/anat/sub-06_ses-010_acq-coronal_localizer.json create mode 120000 sub-06/ses-010/anat/sub-06_ses-010_acq-coronal_localizer.nii.gz create mode 100644 sub-06/ses-010/anat/sub-06_ses-010_acq-sagittal_localizer.json create mode 120000 sub-06/ses-010/anat/sub-06_ses-010_acq-sagittal_localizer.nii.gz create mode 100644 sub-06/ses-010/anat/sub-06_ses-010_scout.json create mode 120000 sub-06/ses-010/anat/sub-06_ses-010_scout.nii.gz create mode 100644 sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-06/ses-010/sub-06_ses-010_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 02c6cd092..75ef3171f 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 02c6cd09237a3cd8c72bc260cb6a1bb9ad734e10 +Subproject commit 75ef3171f19a551dd2d7eb808a4e1bbf2b14b371 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..db37a3f34 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-06 41 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-06/ses-010/anat/sub-06_ses-010_acq-axial_localizer.json b/sub-06/ses-010/anat/sub-06_ses-010_acq-axial_localizer.json new file mode 100644 index 000000000..97f5b3d2c --- /dev/null +++ b/sub-06/ses-010/anat/sub-06_ses-010_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:15:55.115000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.031598, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 240.192 +} \ No newline at end of file diff --git a/sub-06/ses-010/anat/sub-06_ses-010_acq-axial_localizer.nii.gz b/sub-06/ses-010/anat/sub-06_ses-010_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..9ded6c2fb --- /dev/null +++ b/sub-06/ses-010/anat/sub-06_ses-010_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/V1/M9/MD5E-s168401--87d563c8cb97c22170e30547eeb1a047.nii.gz/MD5E-s168401--87d563c8cb97c22170e30547eeb1a047.nii.gz \ No newline at end of file diff --git a/sub-06/ses-010/anat/sub-06_ses-010_acq-coronal_localizer.json b/sub-06/ses-010/anat/sub-06_ses-010_acq-coronal_localizer.json new file mode 100644 index 000000000..f41ff49aa --- /dev/null +++ b/sub-06/ses-010/anat/sub-06_ses-010_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:16:2.105000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, 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"SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 240.192 +} \ No newline at end of file diff --git a/sub-06/ses-010/anat/sub-06_ses-010_acq-coronal_localizer.nii.gz b/sub-06/ses-010/anat/sub-06_ses-010_acq-coronal_localizer.nii.gz new file mode 120000 index 000000000..09ec225bd --- /dev/null +++ b/sub-06/ses-010/anat/sub-06_ses-010_acq-coronal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Gk/fm/MD5E-s194218--7cfa00a4979de234b8cc9ddf2b0d1b96.nii.gz/MD5E-s194218--7cfa00a4979de234b8cc9ddf2b0d1b96.nii.gz \ No newline at end of file diff --git a/sub-06/ses-010/anat/sub-06_ses-010_acq-sagittal_localizer.json b/sub-06/ses-010/anat/sub-06_ses-010_acq-sagittal_localizer.json new file mode 100644 index 000000000..1336516f0 --- /dev/null +++ b/sub-06/ses-010/anat/sub-06_ses-010_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:15:48.125000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 0, + 1, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Sag", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + 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a/sub-06/ses-010/anat/sub-06_ses-010_acq-sagittal_localizer.nii.gz b/sub-06/ses-010/anat/sub-06_ses-010_acq-sagittal_localizer.nii.gz new file mode 120000 index 000000000..0959de67a --- /dev/null +++ b/sub-06/ses-010/anat/sub-06_ses-010_acq-sagittal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Fg/f8/MD5E-s611821--ae18d4685b8d976f8f721e35082886ac.nii.gz/MD5E-s611821--ae18d4685b8d976f8f721e35082886ac.nii.gz \ No newline at end of file diff --git a/sub-06/ses-010/anat/sub-06_ses-010_scout.json b/sub-06/ses-010/anat/sub-06_ses-010_scout.json new file mode 100644 index 000000000..ad311c567 --- /dev/null +++ b/sub-06/ses-010/anat/sub-06_ses-010_scout.json @@ -0,0 +1,542 @@ +{ + "AcquisitionMatrixPE": 160, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:15:32.985000", + "BaseResolution": 160, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + 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"dcmmeta_version": 0.6} \ No newline at end of file From a6762ec2f044cda329e6c26ec9cadfb93416e90a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:16:40 -0400 Subject: [PATCH 303/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-06_ses-007_acq-axial_localizer.json | 81 +++ .../sub-06_ses-007_acq-axial_localizer.nii.gz | 1 + .../sub-06_ses-007_acq-coronal_localizer.json | 81 +++ ...ub-06_ses-007_acq-coronal_localizer.nii.gz | 1 + ...sub-06_ses-007_acq-sagittal_localizer.json | 86 +++ ...b-06_ses-007_acq-sagittal_localizer.nii.gz | 1 + sub-06/ses-007/anat/sub-06_ses-007_scout.json | 542 ++++++++++++++++++ .../ses-007/anat/sub-06_ses-007_scout.nii.gz | 1 + ...7_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ...-007_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...07_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...007_task-mario3_run-01_part-mag_events.tsv | 1 + ...007_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...07_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-01_part-phase_events.tsv | 1 + ...7_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-007_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...07_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...007_task-mario3_run-02_part-mag_events.tsv | 1 + ...007_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...07_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-02_part-phase_events.tsv | 1 + ...7_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + sub-06/ses-007/sub-06_ses-007_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 51 files changed, 3485 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-06/ses-007/anat/sub-06_ses-007_acq-axial_localizer.json create mode 120000 sub-06/ses-007/anat/sub-06_ses-007_acq-axial_localizer.nii.gz create mode 100644 sub-06/ses-007/anat/sub-06_ses-007_acq-coronal_localizer.json create mode 120000 sub-06/ses-007/anat/sub-06_ses-007_acq-coronal_localizer.nii.gz create mode 100644 sub-06/ses-007/anat/sub-06_ses-007_acq-sagittal_localizer.json create mode 120000 sub-06/ses-007/anat/sub-06_ses-007_acq-sagittal_localizer.nii.gz create mode 100644 sub-06/ses-007/anat/sub-06_ses-007_scout.json create mode 120000 sub-06/ses-007/anat/sub-06_ses-007_scout.nii.gz create mode 100644 sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_part-phase_sbref.nii.gz create mode 120000 sub-06/ses-007/sub-06_ses-007_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index cc4a2d205..2b5fc186e 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit cc4a2d205f67c75ce6cef8e471846dcd8031efd4 +Subproject commit 2b5fc186e96e9a7822a988f8b0a8ab6273f991b1 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..db37a3f34 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-06 41 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-06/ses-007/anat/sub-06_ses-007_acq-axial_localizer.json b/sub-06/ses-007/anat/sub-06_ses-007_acq-axial_localizer.json new file mode 100644 index 000000000..cdb249aa2 --- /dev/null +++ b/sub-06/ses-007/anat/sub-06_ses-007_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:53:32.070000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0352418, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 251.463 +} \ No newline at end of file diff --git a/sub-06/ses-007/anat/sub-06_ses-007_acq-axial_localizer.nii.gz b/sub-06/ses-007/anat/sub-06_ses-007_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..275d234fd --- /dev/null +++ b/sub-06/ses-007/anat/sub-06_ses-007_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/2x/Zq/MD5E-s163976--0c9ca907b46c42925c2aa9381c52a37f.nii.gz/MD5E-s163976--0c9ca907b46c42925c2aa9381c52a37f.nii.gz \ No newline at end of file diff --git a/sub-06/ses-007/anat/sub-06_ses-007_acq-coronal_localizer.json b/sub-06/ses-007/anat/sub-06_ses-007_acq-coronal_localizer.json new file mode 100644 index 000000000..d813f7881 --- /dev/null +++ b/sub-06/ses-007/anat/sub-06_ses-007_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:53:39.060000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": 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a/sub-06/ses-007/anat/sub-06_ses-007_acq-sagittal_localizer.json b/sub-06/ses-007/anat/sub-06_ses-007_acq-sagittal_localizer.json new file mode 100644 index 000000000..f04032411 --- /dev/null +++ b/sub-06/ses-007/anat/sub-06_ses-007_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:53:25.080000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 0, + 1, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Sag", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0352418, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SliceTiming": [ + 0, + 10.4844, + 3.5 + ], + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 28, + "StationName": "MRC35049", + "TxRefAmp": 251.463 +} \ No newline at end of file diff --git a/sub-06/ses-007/anat/sub-06_ses-007_acq-sagittal_localizer.nii.gz b/sub-06/ses-007/anat/sub-06_ses-007_acq-sagittal_localizer.nii.gz new file mode 120000 index 000000000..40a838956 --- /dev/null +++ b/sub-06/ses-007/anat/sub-06_ses-007_acq-sagittal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/g3/p9/MD5E-s600189--a08e1a1eaebabee3fce0adb537e4d134.nii.gz/MD5E-s600189--a08e1a1eaebabee3fce0adb537e4d134.nii.gz \ No newline at end of file diff --git a/sub-06/ses-007/anat/sub-06_ses-007_scout.json b/sub-06/ses-007/anat/sub-06_ses-007_scout.json new file mode 100644 index 000000000..ec1f3a0f2 --- /dev/null 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0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From ded0aba151487d4939f595e09e88812d7ceca9c4 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:16:42 -0400 Subject: [PATCH 304/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-017_acq-axial_localizer.json | 81 +++ .../sub-02_ses-017_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-017_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-017_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-017_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-017_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-017/anat/sub-02_ses-017_scout.json | 542 ++++++++++++++++++ .../ses-017/anat/sub-02_ses-017_scout.nii.gz | 1 + ...7_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-06_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-06_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-07_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-07_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-07_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-07_part-phase_epi.nii.gz | 1 + ...-017_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...017_task-mario3_run-01_part-mag_events.tsv | 1 + ...017_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-01_part-phase_events.tsv | 1 + ...7_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-017_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...017_task-mario3_run-02_part-mag_events.tsv | 1 + ...017_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-02_part-phase_events.tsv | 1 + ...7_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-017_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...017_task-mario3_run-03_part-mag_events.tsv | 1 + ...017_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-03_part-phase_events.tsv | 1 + ...7_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-017_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...017_task-mario3_run-04_part-mag_events.tsv | 1 + ...017_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-04_part-phase_events.tsv | 1 + ...7_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-017_task-mario3_run-05_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...017_task-mario3_run-05_part-mag_events.tsv | 1 + ...017_task-mario3_run-05_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-05_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-05_part-phase_events.tsv | 1 + ...7_task-mario3_run-05_part-phase_sbref.json | 153 +++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + ...-017_task-mario3_run-06_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-06_part-mag_bold.nii.gz | 1 + ...017_task-mario3_run-06_part-mag_events.tsv | 1 + ...017_task-mario3_run-06_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-06_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-06_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-06_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-06_part-phase_events.tsv | 1 + ...7_task-mario3_run-06_part-phase_sbref.json | 153 +++++ ...task-mario3_run-06_part-phase_sbref.nii.gz | 1 + ...-017_task-mario3_run-07_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-07_part-mag_bold.nii.gz | 1 + ...017_task-mario3_run-07_part-mag_events.tsv | 1 + ...017_task-mario3_run-07_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-07_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-07_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-07_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-07_part-phase_events.tsv | 1 + ...7_task-mario3_run-07_part-phase_sbref.json | 153 +++++ ...task-mario3_run-07_part-phase_sbref.nii.gz | 1 + sub-02/ses-017/sub-02_ses-017_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 121 files changed, 8295 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-017/anat/sub-02_ses-017_acq-axial_localizer.json create mode 120000 sub-02/ses-017/anat/sub-02_ses-017_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-017/anat/sub-02_ses-017_acq-coronal_localizer.json create mode 120000 sub-02/ses-017/anat/sub-02_ses-017_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-017/anat/sub-02_ses-017_acq-sagittal_localizer.json create mode 120000 sub-02/ses-017/anat/sub-02_ses-017_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-017/anat/sub-02_ses-017_scout.json create mode 120000 sub-02/ses-017/anat/sub-02_ses-017_scout.nii.gz create mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.json create mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz create mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.json create mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz create mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_part-mag_epi.json create mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz create mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_part-phase_epi.json create mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz create mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_part-mag_epi.json create mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz create mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_part-phase_epi.json create mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_part-mag_bold.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_part-mag_bold.nii.gz create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_part-mag_events.tsv create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_part-mag_sbref.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_part-phase_bold.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_part-phase_bold.nii.gz create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_part-phase_events.tsv create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_part-phase_sbref.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_part-mag_bold.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_part-mag_bold.nii.gz create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_part-mag_events.tsv create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_part-mag_sbref.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_part-phase_bold.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_part-phase_bold.nii.gz create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_part-phase_events.tsv create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_part-phase_sbref.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-mag_bold.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-mag_bold.nii.gz create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-mag_events.tsv create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-mag_sbref.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-phase_bold.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-phase_bold.nii.gz create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-phase_events.tsv create mode 100644 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-phase_sbref.json create mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-phase_sbref.nii.gz create mode 120000 sub-02/ses-017/sub-02_ses-017_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 6d8c7a6ee..d5d2160a6 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 6d8c7a6ee4a143c9feab79a9736cf3bc0837d9ef +Subproject commit d5d2160a65581e0db738bde2d89d74828a26d245 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..83ada7a9d --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 51 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-017/anat/sub-02_ses-017_acq-axial_localizer.json b/sub-02/ses-017/anat/sub-02_ses-017_acq-axial_localizer.json new file mode 100644 index 000000000..6cea150a0 --- /dev/null +++ b/sub-02/ses-017/anat/sub-02_ses-017_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:37:36.037500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + 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b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-phase_sbref.nii.gz new file mode 120000 index 000000000..691b99e18 --- /dev/null +++ b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/w3/1m/MD5E-s1103164--ce0e4c12e6d03b6a570fba2bbd062154.nii.gz/MD5E-s1103164--ce0e4c12e6d03b6a570fba2bbd062154.nii.gz \ No newline at end of file diff --git a/sub-02/ses-017/sub-02_ses-017_scans.tsv b/sub-02/ses-017/sub-02_ses-017_scans.tsv new file mode 120000 index 000000000..5de6fc724 --- /dev/null +++ b/sub-02/ses-017/sub-02_ses-017_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/PX/64/MD5E-s5155--1a439d953cf192b10b495bf0b9601b05.tsv/MD5E-s5155--1a439d953cf192b10b495bf0b9601b05.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..4cd1edbdd --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.998976, 0.00436785, 0.0450351, 0.018658, 0.866997, -0.497963], + "ImageOrientationText": "Tra>Cor(-29.9)>Sag(2.4)", + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0476098, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [609, -7197, -8842, 267, 17, -136, -37, 47], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 255.929, + "dcmmeta_affine": [ + [-1.9979517459869385, 0.03731606900691986, 0.08244072645902634, 103.4779052734375], + [-0.008735701441764832, 1.7339946031570435, -0.9965872764587402, -51.00688171386719], + [0.09007024765014648, 0.9959267377853394, 1.7320557832717896, -81.2717514038086], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 88d3f35fa137be70db6fc57e4133bd1adbf74664 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:17:47 -0400 Subject: [PATCH 305/463] fix fmap phase --- ...6_ses-007_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-007_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-007_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-007_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-007_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - sub-06/ses-007/sub-06_ses-007_scans.tsv | 2 +- 17 files changed, 1 insertion(+), 638 deletions(-) rename sub-06/ses-007/fmap/{sub-06_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-06_ses-007_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-007/fmap/{sub-06_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-007_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-007/fmap/{sub-06_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-06_ses-007_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-007/fmap/{sub-06_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-007_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-007/fmap/{sub-06_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-06_ses-007_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-06/ses-007/fmap/{sub-06_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-06_ses-007_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-06/ses-007/fmap/{sub-06_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-06_ses-007_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-06/ses-007/fmap/{sub-06_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-06_ses-007_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz diff --git a/sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index b50ab2e59..000000000 --- a/sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:54:34.582500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999129, -0.0416066, 0.00312938, 0.0401292, 0.93769, -0.345148], - "ImageOrientationText": "Tra>Cor(-20.2)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0413966, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [630, 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b/sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index f9d4403aa..000000000 --- a/sub-06/ses-007/fmap/sub-06_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/8m/ZZ/MD5E-s3335263--3af5bab19ea93c89dc3a1ed6aaffc23c.nii.gz/MD5E-s3335263--3af5bab19ea93c89dc3a1ed6aaffc23c.nii.gz \ No newline at end of file diff --git a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 178edcfe8..000000000 --- a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:54:24.152500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999129, - -0.0416066, - 0.00312938, - 0.0401292, - 0.93769, - -0.345148 - ], - "ImageOrientationText": "Tra>Cor(-20.2)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0413966, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 630, - -7251, - -8833, - 530, - 22, - -217, - -147, - 11 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.463, - "WipMemBlock": "7ca7be37-1c23-4a85-8ebb-f568f6c0d9a5||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index b32131e13..000000000 --- a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/0M/8f/MD5E-s1112466--1bcc6bdc86a1ed13b5d1fdcc683cabf3.nii.gz/MD5E-s1112466--1bcc6bdc86a1ed13b5d1fdcc683cabf3.nii.gz \ No newline at end of file diff --git a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index f7b1af88e..000000000 --- a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:55:34.705000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999129, - -0.0416066, - 0.00312938, - 0.0401292, - 0.93769, - -0.345148 - ], - "ImageOrientationText": "Tra>Cor(-20.2)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0519077, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 630, - -7251, - -8833, - 530, - 22, - -217, - -147, - 11 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.463, - "WipMemBlock": "7e84574a-6df1-406c-8e5f-d7cd2f675f87||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 1ecf1c8b7..000000000 --- a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/1Q/2J/MD5E-s1103688--af3479fd2f1bff015eaca6c30426ea47.nii.gz/MD5E-s1103688--af3479fd2f1bff015eaca6c30426ea47.nii.gz \ No newline at end of file diff --git a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 4b12ac978..000000000 --- a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:15:8.532500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999129, - -0.0416066, - 0.00312938, - 0.0401292, - 0.93769, - -0.345148 - ], - "ImageOrientationText": "Tra>Cor(-20.2)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0519077, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 630, - -7251, - -8833, - 530, - 22, - -217, - -147, - 11 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.463, - "WipMemBlock": "7e702a9d-fbfb-4906-9cbb-0dc108e1bc11||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 210dfacf4..000000000 --- a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Mq/P1/MD5E-s1103625--bb9b12caceeafe77f6ddf259b5aa3124.nii.gz/MD5E-s1103625--bb9b12caceeafe77f6ddf259b5aa3124.nii.gz \ No newline at end of file diff --git a/sub-06/ses-007/sub-06_ses-007_scans.tsv b/sub-06/ses-007/sub-06_ses-007_scans.tsv index 0f4982f8a..3329074ab 120000 --- a/sub-06/ses-007/sub-06_ses-007_scans.tsv +++ b/sub-06/ses-007/sub-06_ses-007_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/jq/fk/MD5E-s2045--fdf4492686ca8c7900f8f560ae97a8d6.tsv/MD5E-s2045--fdf4492686ca8c7900f8f560ae97a8d6.tsv \ No newline at end of file +../../.git/annex/objects/zp/mk/MD5E-s1565--ea2cc46358d17833b748d80f4106740d.tsv/MD5E-s1565--ea2cc46358d17833b748d80f4106740d.tsv \ No newline at end of file From c1cdc09e82ac36577fcf3b4ea829a0b2dc4b674f Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:17:47 -0400 Subject: [PATCH 306/463] fix fmap phase --- ...6_ses-010_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-010_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-010_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-010_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-010_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-010_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-06/ses-010/sub-06_ses-010_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-06/ses-010/fmap/{sub-06_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-06_ses-010_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-010/fmap/{sub-06_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-010_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-010/fmap/{sub-06_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-06_ses-010_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-010/fmap/{sub-06_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-010_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-010/fmap/{sub-06_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-06_ses-010_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-06/ses-010/fmap/{sub-06_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-06_ses-010_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-06/ses-010/fmap/{sub-06_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-06_ses-010_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-06/ses-010/fmap/{sub-06_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-06_ses-010_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-06/ses-010/fmap/{sub-06_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-06_ses-010_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-06/ses-010/fmap/{sub-06_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-06_ses-010_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index b3929cdc6..000000000 --- a/sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:16:57.855000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.998289, -0.0579381, 0.00792403, 0.0572113, 0.939621, -0.337401], - "ImageOrientationText": 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ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.996577501296997, 0.11442263424396515, -0.02420557662844658, 101.27952575683594], - [0.11587617546319962, 1.879241704940796, -0.6745540499687195, -71.4219970703125], - [0.015848061069846153, 0.6748021245002747, 1.8826552629470825, -63.40589904785156], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99828872962102, -0.057938088062, 0.00792403075265, 0.0572113173045, 0.93962087171985, 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"ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "161744.263000", - "SliceLocation": -36.822492591974, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999533534, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "161459.332000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["161657.855000", "161659.345000", "161700.835000"], - "ContentTime": ["161744.265000", "161744.268000", "161744.270000"], - "InstanceCreationTime": ["161744.265000", "161744.268000", "161744.270000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4816.0, 4814.0, 4790.0], - "WindowWidth": [18598.0, 18600.0, 18566.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 031041e50..000000000 --- a/sub-06/ses-010/fmap/sub-06_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/xZ/0v/MD5E-s3334630--d64a69ca6a50501a4453ecbd551f5312.nii.gz/MD5E-s3334630--d64a69ca6a50501a4453ecbd551f5312.nii.gz \ No newline at end of file diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 8a94bf78a..000000000 --- a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:16:47.425000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998289, - -0.0579381, - 0.00792403, - 0.0572113, - 0.939621, - -0.337401 - ], - "ImageOrientationText": "Tra>Cor(-19.7)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0371164, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 637, - -7265, - -8828, - 512, - 38, - -240, - -89, - 3 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 240.192, - "WipMemBlock": "cd1b590c-bce6-46e6-90ae-68365507dbb3||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 7c6f68ca5..000000000 --- a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/17/06/MD5E-s1112381--d39d6eed1af35ac55d2cbb142f4ec07e.nii.gz/MD5E-s1112381--d39d6eed1af35ac55d2cbb142f4ec07e.nii.gz \ No newline at end of file diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index e582f6b33..000000000 --- a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:18:21.747500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998289, - -0.0579381, - 0.00792403, - 0.0572113, - 0.939621, - -0.337401 - ], - "ImageOrientationText": "Tra>Cor(-19.7)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0465407, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 637, - -7265, - -8828, - 512, - 38, - -240, - -89, - 3 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 240.192, - "WipMemBlock": "30bfd655-b176-4fb8-90ca-a6e0dd51a33f||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 23efa66d4..000000000 --- a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/jG/06/MD5E-s1103618--5f40ec885589d6517e3a23d00d17d03f.nii.gz/MD5E-s1103618--5f40ec885589d6517e3a23d00d17d03f.nii.gz \ No newline at end of file diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index ae34516fd..000000000 --- a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:29:53.530000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998289, - -0.0579381, - 0.00792403, - 0.0572113, - 0.939621, - -0.337401 - ], - "ImageOrientationText": "Tra>Cor(-19.7)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0465407, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 637, - -7265, - -8828, - 512, - 38, - -240, - -89, - 3 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 240.192, - "WipMemBlock": "2784a290-1753-46e7-8f8a-50a90ebfd7d8||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 9ff1c6ffb..000000000 --- a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Wx/5x/MD5E-s1103573--7d63051462f909b6f4552f883feac6af.nii.gz/MD5E-s1103573--7d63051462f909b6f4552f883feac6af.nii.gz \ No newline at end of file diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 325ec679a..000000000 --- a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:41:26.117500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998289, - -0.0579381, - 0.00792403, - 0.0572113, - 0.939621, - -0.337401 - ], - "ImageOrientationText": "Tra>Cor(-19.7)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0465407, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 637, - -7265, - -8828, - 512, - 38, - -240, - -89, - 3 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 240.192, - "WipMemBlock": "9dabca42-1c16-496d-9163-bb66b359e9c0||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 555115c7f..000000000 --- a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/5K/8q/MD5E-s1103434--0b01c8cfd2b760a13131d039b2d053d0.nii.gz/MD5E-s1103434--0b01c8cfd2b760a13131d039b2d053d0.nii.gz \ No newline at end of file diff --git a/sub-06/ses-010/sub-06_ses-010_scans.tsv b/sub-06/ses-010/sub-06_ses-010_scans.tsv index a625bd66a..fd9e86f98 120000 --- a/sub-06/ses-010/sub-06_ses-010_scans.tsv +++ b/sub-06/ses-010/sub-06_ses-010_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/3W/0M/MD5E-s2667--fef4b78d47e8548a1a53ede6aa876a23.tsv/MD5E-s2667--fef4b78d47e8548a1a53ede6aa876a23.tsv \ No newline at end of file +../../.git/annex/objects/08/GZ/MD5E-s2066--d2596ba7fea3a9c04e1e3fb3e60b259b.tsv/MD5E-s2066--d2596ba7fea3a9c04e1e3fb3e60b259b.tsv \ No newline at end of file From 75e5a100e0466323071c006464e6a4d323a51fe7 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:18:05 -0400 Subject: [PATCH 307/463] fix complex event files --- ...g_events.tsv => sub-06_ses-007_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-06_ses-007_task-mario3_run-02_events.tsv} | 0 .../func/sub-06_ses-007_task-mario3_run-02_part-mag_events.tsv | 1 - .../func/sub-06_ses-007_task-mario3_run-02_part-phase_events.tsv | 1 - 4 files changed, 2 deletions(-) rename sub-06/ses-007/func/{sub-06_ses-007_task-mario3_run-01_part-mag_events.tsv => sub-06_ses-007_task-mario3_run-01_events.tsv} (100%) rename sub-06/ses-007/func/{sub-06_ses-007_task-mario3_run-01_part-phase_events.tsv => sub-06_ses-007_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_part-mag_events.tsv delete mode 120000 sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_part-phase_events.tsv diff --git a/sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-01_part-mag_events.tsv b/sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-01_events.tsv similarity index 100% rename from sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-01_part-mag_events.tsv rename to sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-01_events.tsv diff --git a/sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-01_part-phase_events.tsv b/sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_events.tsv similarity index 100% rename from sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-01_part-phase_events.tsv rename to sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_events.tsv diff --git a/sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_part-mag_events.tsv b/sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_part-phase_events.tsv b/sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-007/func/sub-06_ses-007_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 167768952ee7efc42f01b17e02f7d626249cc01b Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:18:06 -0400 Subject: [PATCH 308/463] fix fmap phase --- ...2_ses-017_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-017_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-017_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-06_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-06_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-07_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-07_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-07_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-07_part-phase_epi.nii.gz | 1 - sub-02/ses-017/sub-02_ses-017_scans.tsv | 2 +- 37 files changed, 1 insertion(+), 1403 deletions(-) rename sub-02/ses-017/fmap/{sub-02_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-017_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-017/fmap/{sub-02_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-017_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-017/fmap/{sub-02_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-017_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-017/fmap/{sub-02_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-017_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-017/fmap/{sub-02_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-017_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-017/fmap/{sub-02_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-017_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-017/fmap/{sub-02_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-017_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-017/fmap/{sub-02_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-017_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-017/fmap/{sub-02_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-017_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-017/fmap/{sub-02_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-017_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-02/ses-017/fmap/{sub-02_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-02_ses-017_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-02/ses-017/fmap/{sub-02_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-02_ses-017_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-02/ses-017/fmap/{sub-02_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-02_ses-017_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-02/ses-017/fmap/{sub-02_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-02_ses-017_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz rename sub-02/ses-017/fmap/{sub-02_ses-017_acq-sbref_dir-PA_run-06_part-mag_epi.json => sub-02_ses-017_acq-sbref_dir-PA_run-06_epi.json} (100%) rename sub-02/ses-017/fmap/{sub-02_ses-017_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz => sub-02_ses-017_acq-sbref_dir-PA_run-06_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_part-phase_epi.json delete mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz rename sub-02/ses-017/fmap/{sub-02_ses-017_acq-sbref_dir-PA_run-07_part-mag_epi.json => sub-02_ses-017_acq-sbref_dir-PA_run-07_epi.json} (100%) rename sub-02/ses-017/fmap/{sub-02_ses-017_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz => sub-02_ses-017_acq-sbref_dir-PA_run-07_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_part-phase_epi.json delete mode 120000 sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index f1161335d..000000000 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:38:45.570000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.998976, 0.00436785, 0.0450351, 0.018658, 0.866997, -0.497963], - "ImageOrientationText": "Tra>Cor(-29.9)>Sag(2.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.037969, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [609, -7197, -8842, 267, 17, -136, -37, 47], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 255.929, - "WipMemBlock": "2998ac39-c9a0-444f-85a1-4b716b5b719e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9979517459869385, 0.03731606900691986, 0.08244072645902634, 103.4779052734375], - [-0.008735701441764832, 1.7339946031570435, -0.9965872764587402, -51.00688171386719], - [0.09007024765014648, 0.9959267377853394, 1.7320557832717896, -81.2717514038086], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99897585531251, 0.00436785049315, 0.04503512390017, 0.01865803532478, 0.86699733101836, -0.4979633578135], - "ImagePositionPatient": [-848.15893522872, -761.94842241773, 351.04045321352], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.260183, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "151911.717000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.03796902922793, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "153931.126000", - "SliceLocation": -40.701805237793, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999971411, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "151911.639000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["153845.570000", "153847.060000", "153848.550000"], - "ContentTime": ["153931.128000", "153931.131000", "153931.134000"], - "InstanceCreationTime": ["153931.128000", "153931.131000", "153931.134000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4928.0, 4924.0, 4946.0], - "WindowWidth": [18674.0, 18658.0, 18724.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 7346fa10e..000000000 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/PZ/53/MD5E-s3333369--13be57ed8b93d8a1db032244c8cebf11.nii.gz/MD5E-s3333369--13be57ed8b93d8a1db032244c8cebf11.nii.gz \ No newline at end of file diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 157377a5f..000000000 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:38:35.140000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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"PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.037969, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 609, - -7197, - -8842, - 267, - 17, - -136, - -37, - 47 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 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-../../../.git/annex/objects/G4/v9/MD5E-s1112165--c80c4b9b5b8e903778ff53a562856b1d.nii.gz/MD5E-s1112165--c80c4b9b5b8e903778ff53a562856b1d.nii.gz \ No newline at end of file diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index ab6de9b77..000000000 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:40:51.437500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998976, - 0.00436785, - 0.0450351, - 0.018658, - 0.866997, - -0.497963 - ], - "ImageOrientationText": "Tra>Cor(-29.9)>Sag(2.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0476098, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 609, - -7197, - -8842, - 267, - 17, - -136, - -37, - 47 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 255.929, - "WipMemBlock": "c4f4adcf-733d-4e59-a650-d74ba1424a54||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 783caefb8..000000000 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/xg/kf/MD5E-s1103365--10f627b910469395c0c74f5c711cc9ac.nii.gz/MD5E-s1103365--10f627b910469395c0c74f5c711cc9ac.nii.gz \ No newline at end of file diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 668316fef..000000000 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:52:4.145000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998976, - 0.00436785, - 0.0450351, - 0.018658, - 0.866997, - -0.497963 - ], - "ImageOrientationText": "Tra>Cor(-29.9)>Sag(2.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - 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"SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 609, - -7197, - -8842, - 267, - 17, - -136, - -37, - 47 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 255.929, - "WipMemBlock": "2d02dede-cccf-49c0-b052-43f2661bbbdc||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 2cab39659..000000000 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Pw/w8/MD5E-s1103207--3de16292ae71ab3e879eaab5f0ae662b.nii.gz/MD5E-s1103207--3de16292ae71ab3e879eaab5f0ae662b.nii.gz \ No newline at end of file diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 2f20df684..000000000 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:01:6.555000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of 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b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index e8fae3b2e..000000000 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Px/kV/MD5E-s1103286--da6758ecab5f8993a0fa62363790f858.nii.gz/MD5E-s1103286--da6758ecab5f8993a0fa62363790f858.nii.gz \ No newline at end of file diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index f7c193bdd..000000000 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:09:28.077500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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-../../../.git/annex/objects/MX/k8/MD5E-s1103227--67fbc84f69b23525a0f0c60bbf9c2b56.nii.gz/MD5E-s1103227--67fbc84f69b23525a0f0c60bbf9c2b56.nii.gz \ No newline at end of file diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index fb96b718d..000000000 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:19:34.460000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 255.929, - "WipMemBlock": "208314e3-0776-4429-8dcb-ffabad4632e7||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index 4710616cb..000000000 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/7P/vX/MD5E-s1103140--715c9537edd41ced3ee4763f6e619014.nii.gz/MD5E-s1103140--715c9537edd41ced3ee4763f6e619014.nii.gz \ No newline at end of file diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_part-mag_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_epi.json similarity index 100% rename from sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_part-mag_epi.json rename to sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_epi.json diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_epi.nii.gz similarity index 100% rename from sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz rename to sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_epi.nii.gz diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_part-phase_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_part-phase_epi.json deleted file mode 100644 index c67119ebe..000000000 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:30:19.375000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998976, - 0.00436785, - 0.0450351, - 0.018658, - 0.866997, - -0.497963 - ], - "ImageOrientationText": "Tra>Cor(-29.9)>Sag(2.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - 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"SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-06_SBRef", - "SeriesNumber": 24, - "ShimSetting": [ - 609, - -7197, - -8842, - 267, - 17, - -136, - -37, - 47 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 255.929, - "WipMemBlock": "47ffd644-189e-4b69-973b-f962c9018d72||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz deleted file mode 120000 index 0c8e934cc..000000000 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/M6/j8/MD5E-s1103304--7f85a5664346fa4618e617ec4e6c441c.nii.gz/MD5E-s1103304--7f85a5664346fa4618e617ec4e6c441c.nii.gz \ No newline at end of file diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_part-mag_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_epi.json similarity index 100% rename from sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_part-mag_epi.json rename to sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_epi.json diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_epi.nii.gz similarity index 100% rename from sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz rename to sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_epi.nii.gz diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_part-phase_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_part-phase_epi.json deleted file mode 100644 index d562b20fa..000000000 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:40:11.080000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998976, - 0.00436785, - 0.0450351, - 0.018658, - 0.866997, - -0.497963 - ], - "ImageOrientationText": "Tra>Cor(-29.9)>Sag(2.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-07", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0476098, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-07_SBRef", - "SeriesNumber": 27, - "ShimSetting": [ - 609, - -7197, - -8842, - 267, - 17, - -136, - -37, - 47 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 255.929, - "WipMemBlock": "94cea7cd-6d75-4bab-8157-d4ff12732684||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz deleted file mode 120000 index 691b99e18..000000000 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/w3/1m/MD5E-s1103164--ce0e4c12e6d03b6a570fba2bbd062154.nii.gz/MD5E-s1103164--ce0e4c12e6d03b6a570fba2bbd062154.nii.gz \ No newline at end of file diff --git a/sub-02/ses-017/sub-02_ses-017_scans.tsv b/sub-02/ses-017/sub-02_ses-017_scans.tsv index 5de6fc724..0c1ba74fc 120000 --- a/sub-02/ses-017/sub-02_ses-017_scans.tsv +++ b/sub-02/ses-017/sub-02_ses-017_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/PX/64/MD5E-s5155--1a439d953cf192b10b495bf0b9601b05.tsv/MD5E-s5155--1a439d953cf192b10b495bf0b9601b05.tsv \ No newline at end of file +../../.git/annex/objects/q2/7f/MD5E-s4070--5da4d3680fa8629e1c7efafaedd6ee71.tsv/MD5E-s4070--5da4d3680fa8629e1c7efafaedd6ee71.tsv \ No newline at end of file From da9c21675e6dd6a8d8c37d6a8bff3289392f50af Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:18:06 -0400 Subject: [PATCH 309/463] fix complex event files --- ...g_events.tsv => sub-06_ses-010_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-06_ses-010_task-mario3_run-02_events.tsv} | 0 .../func/sub-06_ses-010_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-06_ses-010_task-mario3_run-03_events.tsv} | 0 .../func/sub-06_ses-010_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-06_ses-010_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-06/ses-010/func/{sub-06_ses-010_task-mario3_run-01_part-mag_events.tsv => sub-06_ses-010_task-mario3_run-01_events.tsv} (100%) rename sub-06/ses-010/func/{sub-06_ses-010_task-mario3_run-01_part-phase_events.tsv => sub-06_ses-010_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-02_part-phase_events.tsv rename sub-06/ses-010/func/{sub-06_ses-010_task-mario3_run-02_part-mag_events.tsv => sub-06_ses-010_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-01_part-mag_events.tsv b/sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-01_events.tsv similarity index 100% rename from sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-01_part-mag_events.tsv rename to sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-01_events.tsv diff --git a/sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-01_part-phase_events.tsv b/sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-02_events.tsv similarity index 100% rename from sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-01_part-phase_events.tsv rename to sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-02_events.tsv diff --git a/sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-02_part-phase_events.tsv b/sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-02_part-mag_events.tsv b/sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_events.tsv similarity index 100% rename from sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-02_part-mag_events.tsv rename to sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_events.tsv diff --git a/sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_part-mag_events.tsv b/sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_part-phase_events.tsv b/sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-010/func/sub-06_ses-010_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From d33f40505491a02ec7a47bc7f3423a5d18fbe0c2 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:18:24 -0400 Subject: [PATCH 310/463] fix complex event files --- ...g_events.tsv => sub-02_ses-017_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-02_ses-017_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-02_ses-017_task-mario3_run-03_events.tsv} | 0 ...e_events.tsv => sub-02_ses-017_task-mario3_run-04_events.tsv} | 0 .../func/sub-02_ses-017_task-mario3_run-04_part-phase_events.tsv | 1 - ...g_events.tsv => sub-02_ses-017_task-mario3_run-05_events.tsv} | 0 .../func/sub-02_ses-017_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-02_ses-017_task-mario3_run-05_part-phase_events.tsv | 1 - ...e_events.tsv => sub-02_ses-017_task-mario3_run-06_events.tsv} | 0 .../func/sub-02_ses-017_task-mario3_run-06_part-mag_events.tsv | 1 - .../func/sub-02_ses-017_task-mario3_run-06_part-phase_events.tsv | 1 - ...g_events.tsv => sub-02_ses-017_task-mario3_run-07_events.tsv} | 0 .../func/sub-02_ses-017_task-mario3_run-07_part-mag_events.tsv | 1 - .../func/sub-02_ses-017_task-mario3_run-07_part-phase_events.tsv | 1 - 14 files changed, 7 deletions(-) rename sub-02/ses-017/func/{sub-02_ses-017_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-017_task-mario3_run-01_events.tsv} (100%) rename sub-02/ses-017/func/{sub-02_ses-017_task-mario3_run-01_part-phase_events.tsv => sub-02_ses-017_task-mario3_run-02_events.tsv} (100%) rename sub-02/ses-017/func/{sub-02_ses-017_task-mario3_run-02_part-mag_events.tsv => sub-02_ses-017_task-mario3_run-03_events.tsv} (100%) rename sub-02/ses-017/func/{sub-02_ses-017_task-mario3_run-02_part-phase_events.tsv => sub-02_ses-017_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_part-phase_events.tsv rename sub-02/ses-017/func/{sub-02_ses-017_task-mario3_run-03_part-mag_events.tsv => sub-02_ses-017_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_part-phase_events.tsv rename sub-02/ses-017/func/{sub-02_ses-017_task-mario3_run-03_part-phase_events.tsv => sub-02_ses-017_task-mario3_run-06_events.tsv} (100%) delete mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_part-mag_events.tsv delete mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_part-phase_events.tsv rename sub-02/ses-017/func/{sub-02_ses-017_task-mario3_run-04_part-mag_events.tsv => sub-02_ses-017_task-mario3_run-07_events.tsv} (100%) delete mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-mag_events.tsv delete mode 120000 sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-phase_events.tsv diff --git a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-02_events.tsv similarity index 100% rename from sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_part-phase_events.tsv rename to sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-02_events.tsv diff --git a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-02_part-mag_events.tsv b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-03_events.tsv similarity index 100% rename from sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-02_part-mag_events.tsv rename to sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-03_events.tsv diff --git a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-02_part-phase_events.tsv b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_events.tsv similarity index 100% rename from sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-02_part-phase_events.tsv rename to sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_events.tsv diff --git a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_part-phase_events.tsv b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-03_part-mag_events.tsv b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_events.tsv similarity index 100% rename from sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-03_part-mag_events.tsv rename to sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_events.tsv diff --git a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_part-mag_events.tsv b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_part-phase_events.tsv b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_events.tsv similarity index 100% rename from sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-03_part-phase_events.tsv rename to sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_events.tsv diff --git a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_part-mag_events.tsv b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_part-phase_events.tsv b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_part-mag_events.tsv b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_events.tsv similarity index 100% rename from sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_part-mag_events.tsv rename to sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_events.tsv diff --git a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-mag_events.tsv b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-phase_events.tsv b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 82bc3ca92c0d9ef812058e1d934082b5d4a422eb Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:18:55 -0400 Subject: [PATCH 311/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..ca87698af --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 04025822-14d3-4e43-b323-f4259e5bd009 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..054ef43f4 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 054ef43f4ed9ed58f239399542134d6c870ac4d6 From a18db617c84d0b93ff534822d287b083afd2b958 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:19:09 -0400 Subject: [PATCH 312/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..2661d3dd7 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = ec3d8293-4e35-499f-9d22-80065db122a5 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..6f8f99e01 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 6f8f99e010561820978d008f26288602486558b0 From 242ee70e55620f33484743129a1fe6cb42e686b2 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:19:16 -0400 Subject: [PATCH 313/463] fill IntendedFor --- ...6_ses-007_acq-sbref_dir-AP_run-01_epi.json | 89 ++----------------- ...6_ses-007_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...6_ses-007_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- 3 files changed, 22 insertions(+), 243 deletions(-) diff --git a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_epi.json b/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_epi.json index f197ead9b..85d2a7bae 100644 --- a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999129, - -0.0416066, - 0.00312938, - 0.0401292, - 0.93769, - -0.345148 - ], + "ImageOrientationPatientDICOM": [0.999129, -0.0416066, 0.00312938, 0.0401292, 0.93769, -0.345148], "ImageOrientationText": "Tra>Cor(-20.2)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,16 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-06_ses-007_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-007/func/sub-06_ses-007_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +64,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 630, - -7251, - -8833, - 530, - 22, - -217, - -147, - 11 - ], + "ShimSetting": [630, -7251, -8833, 530, 22, -217, -147, 11], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_epi.json b/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_epi.json index 2fbe0a009..a3bf2f425 100644 --- a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999129, - -0.0416066, - 0.00312938, - 0.0401292, - 0.93769, - -0.345148 - ], + "ImageOrientationPatientDICOM": [0.999129, -0.0416066, 0.00312938, 0.0401292, 0.93769, -0.345148], "ImageOrientationText": "Tra>Cor(-20.2)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-06_ses-007_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 630, - -7251, - -8833, - 530, - 22, - -217, - -147, - 11 - ], + "ShimSetting": [630, -7251, -8833, 530, 22, -217, -147, 11], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_epi.json b/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_epi.json index 639b78a4b..3c04511f9 100644 --- a/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-06/ses-007/fmap/sub-06_ses-007_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999129, - -0.0416066, - 0.00312938, - 0.0401292, - 0.93769, - -0.345148 - ], + "ImageOrientationPatientDICOM": [0.999129, -0.0416066, 0.00312938, 0.0401292, 0.93769, -0.345148], "ImageOrientationText": "Tra>Cor(-20.2)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-06_ses-007_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 630, - -7251, - -8833, - 530, - 22, - -217, - -147, - 11 - ], + "ShimSetting": [630, -7251, -8833, 530, 22, -217, -147, 11], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.02, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From fcc334806042c7487004dbb66e3f5b56e5e5430a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:19:19 -0400 Subject: [PATCH 314/463] fill IntendedFor --- ...6_ses-010_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...6_ses-010_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...6_ses-010_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...6_ses-010_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_epi.json b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_epi.json index ad4e66731..669f9251c 100644 --- a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998289, - -0.0579381, - 0.00792403, - 0.0572113, - 0.939621, - -0.337401 - ], + "ImageOrientationPatientDICOM": [0.998289, -0.0579381, 0.00792403, 0.0572113, 0.939621, -0.337401], "ImageOrientationText": "Tra>Cor(-19.7)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-06_ses-010_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-010/func/sub-06_ses-010_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-010/func/sub-06_ses-010_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 637, - -7265, - -8828, - 512, - 38, - -240, - -89, - 3 - ], + "ShimSetting": [637, -7265, -8828, 512, 38, -240, -89, 3], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_epi.json b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_epi.json index 7ff034d49..4d138d99d 100644 --- a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998289, - -0.0579381, - 0.00792403, - 0.0572113, - 0.939621, - -0.337401 - ], + "ImageOrientationPatientDICOM": [0.998289, -0.0579381, 0.00792403, 0.0572113, 0.939621, -0.337401], "ImageOrientationText": "Tra>Cor(-19.7)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-06_ses-010_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 637, - -7265, - -8828, - 512, - 38, - -240, - -89, - 3 - ], + "ShimSetting": [637, -7265, -8828, 512, 38, -240, -89, 3], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_epi.json b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_epi.json index 94e7e44ca..aeaf39634 100644 --- a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998289, - -0.0579381, - 0.00792403, - 0.0572113, - 0.939621, - -0.337401 - ], + "ImageOrientationPatientDICOM": [0.998289, -0.0579381, 0.00792403, 0.0572113, 0.939621, -0.337401], "ImageOrientationText": "Tra>Cor(-19.7)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-06_ses-010_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 637, - -7265, - -8828, - 512, - 38, - -240, - -89, - 3 - ], + "ShimSetting": [637, -7265, -8828, 512, 38, -240, -89, 3], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_epi.json b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_epi.json index 9ccc4274d..06f4ab21b 100644 --- a/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-06/ses-010/fmap/sub-06_ses-010_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998289, - -0.0579381, - 0.00792403, - 0.0572113, - 0.939621, - -0.337401 - ], + "ImageOrientationPatientDICOM": [0.998289, -0.0579381, 0.00792403, 0.0572113, 0.939621, -0.337401], "ImageOrientationText": "Tra>Cor(-19.7)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-06_ses-010_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 637, - -7265, - -8828, - 512, - 38, - -240, - -89, - 3 - ], + "ShimSetting": [637, -7265, -8828, 512, 38, -240, -89, 3], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 132a779ac6fd8fa171a813f08f8885b2152d3387 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:19:46 -0400 Subject: [PATCH 315/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-06_ses-014_acq-axial_localizer.json | 81 +++ .../sub-06_ses-014_acq-axial_localizer.nii.gz | 1 + .../sub-06_ses-014_acq-coronal_localizer.json | 81 +++ ...ub-06_ses-014_acq-coronal_localizer.nii.gz | 1 + ...sub-06_ses-014_acq-sagittal_localizer.json | 86 +++ ...b-06_ses-014_acq-sagittal_localizer.nii.gz | 1 + sub-06/ses-014/anat/sub-06_ses-014_scout.json | 542 ++++++++++++++++++ .../ses-014/anat/sub-06_ses-014_scout.nii.gz | 1 + ...4_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-014_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...14_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...014_task-mario3_run-01_part-mag_events.tsv | 1 + ...014_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...14_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-01_part-phase_events.tsv | 1 + ...4_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-014_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...14_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...014_task-mario3_run-02_part-mag_events.tsv | 1 + ...014_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...14_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-02_part-phase_events.tsv | 1 + ...4_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-014_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...14_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...014_task-mario3_run-03_part-mag_events.tsv | 1 + ...014_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...14_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-03_part-phase_events.tsv | 1 + ...4_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-06/ses-014/sub-06_ses-014_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-06/ses-014/anat/sub-06_ses-014_acq-axial_localizer.json create mode 120000 sub-06/ses-014/anat/sub-06_ses-014_acq-axial_localizer.nii.gz create mode 100644 sub-06/ses-014/anat/sub-06_ses-014_acq-coronal_localizer.json create mode 120000 sub-06/ses-014/anat/sub-06_ses-014_acq-coronal_localizer.nii.gz create mode 100644 sub-06/ses-014/anat/sub-06_ses-014_acq-sagittal_localizer.json create mode 120000 sub-06/ses-014/anat/sub-06_ses-014_acq-sagittal_localizer.nii.gz create mode 100644 sub-06/ses-014/anat/sub-06_ses-014_scout.json create mode 120000 sub-06/ses-014/anat/sub-06_ses-014_scout.nii.gz create mode 100644 sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 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100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..db37a3f34 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-06 41 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-06/ses-014/anat/sub-06_ses-014_acq-axial_localizer.json b/sub-06/ses-014/anat/sub-06_ses-014_acq-axial_localizer.json new file mode 100644 index 000000000..6c2ff6964 --- /dev/null +++ b/sub-06/ses-014/anat/sub-06_ses-014_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:20:13.087500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + 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file diff --git a/sub-06/ses-014/anat/sub-06_ses-014_acq-coronal_localizer.json b/sub-06/ses-014/anat/sub-06_ses-014_acq-coronal_localizer.json new file mode 100644 index 000000000..c88f2a532 --- /dev/null +++ b/sub-06/ses-014/anat/sub-06_ses-014_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:20:20.077500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + 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a/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_part-phase_events.tsv b/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_part-phase_events.tsv new file mode 120000 index 000000000..1bbdfddb5 --- /dev/null +++ b/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_part-phase_events.tsv @@ -0,0 +1 @@ +../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_part-phase_sbref.json b/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_part-phase_sbref.json new file mode 100644 index 000000000..627b435f8 --- /dev/null +++ b/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_part-phase_sbref.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:41:37.947500", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTime1": 0.037, + "EchoTime2": 0.001, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Single-band reference", + "ImageOrientationPatientDICOM": [ + 0.998198, + -0.0521176, + 0.0297528, + 0.0593039, + 0.932604, + -0.355996 + ], + "ImageOrientationText": "Tra>Cor(-20.9)>Sag(0.5)", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "P", + "ND", + "MOSAIC", + "PHASE" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "func_task-mario3_run-03", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0475837, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "SeriesDescription": "func_task-mario3_run-03_SBRef", + "SeriesNumber": 15, + "ShimSetting": [ + 628, + -7249, + -8828, + 520, + 14, + -199, + -111, + 7 + ], + 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a/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_part-phase_sbref.nii.gz b/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_part-phase_sbref.nii.gz new file mode 120000 index 000000000..ad4d691e4 --- /dev/null +++ b/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/9f/J9/MD5E-s1103723--b05285ac059cb0f0d205ce62b1883e9f.nii.gz/MD5E-s1103723--b05285ac059cb0f0d205ce62b1883e9f.nii.gz \ No newline at end of file diff --git a/sub-06/ses-014/sub-06_ses-014_scans.tsv b/sub-06/ses-014/sub-06_ses-014_scans.tsv new file mode 120000 index 000000000..69eb7a779 --- /dev/null +++ b/sub-06/ses-014/sub-06_ses-014_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/9f/mZ/MD5E-s2667--a27c10164fc274c996636753c6a1dd33.tsv/MD5E-s2667--a27c10164fc274c996636753c6a1dd33.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..7a25b8c07 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.998198, -0.0521176, 0.0297528, 0.0593039, 0.932604, -0.355996], + "ImageOrientationText": "Tra>Cor(-20.9)>Sag(0.5)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0475837, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [628, -7249, -8828, 520, 14, -199, -111, 7], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 240.65, + "dcmmeta_affine": [ + [-1.996395230293274, 0.11860775947570801, 0.01838778890669346, 100.01006317138672], + [0.10423529148101807, 1.8652076721191406, -0.7142376899719238, -69.22409057617188], + [0.059505585581064224, 0.7119920253753662, 1.8680273294448853, -70.4662857055664], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 308ffeb104582caa0845905c6d44e6b88c72b93e Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:19:50 -0400 Subject: [PATCH 316/463] fill IntendedFor --- ...2_ses-017_acq-sbref_dir-AP_run-01_epi.json | 94 +++---------------- ...2_ses-017_acq-sbref_dir-PA_run-01_epi.json | 88 ++--------------- ...2_ses-017_acq-sbref_dir-PA_run-02_epi.json | 88 ++--------------- ...2_ses-017_acq-sbref_dir-PA_run-03_epi.json | 88 ++--------------- ...2_ses-017_acq-sbref_dir-PA_run-04_epi.json | 88 ++--------------- ...2_ses-017_acq-sbref_dir-PA_run-05_epi.json | 88 ++--------------- ...2_ses-017_acq-sbref_dir-PA_run-06_epi.json | 88 ++--------------- ...2_ses-017_acq-sbref_dir-PA_run-07_epi.json | 88 ++--------------- 8 files changed, 62 insertions(+), 648 deletions(-) diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_epi.json index 6f6e023de..f69cee10c 100644 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998976, - 0.00436785, - 0.0450351, - 0.018658, - 0.866997, - -0.497963 - ], + "ImageOrientationPatientDICOM": [0.998976, 0.00436785, 0.0450351, 0.018658, 0.866997, -0.497963], "ImageOrientationText": "Tra>Cor(-29.9)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,21 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-02_ses-017_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-017/func/sub-02_ses-017_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-017/func/sub-02_ses-017_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-017/func/sub-02_ses-017_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-017/func/sub-02_ses-017_task-mario3_run-05_part-mag_bold.nii.gz", + "ses-017/func/sub-02_ses-017_task-mario3_run-06_part-mag_bold.nii.gz", + "ses-017/func/sub-02_ses-017_task-mario3_run-07_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +69,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 609, - -7197, - -8842, - 267, - 17, - -136, - -37, - 47 - ], + "ShimSetting": [609, -7197, -8842, 267, 17, -136, -37, 47], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_epi.json index 8eeb049d5..e1eaa1ec2 100644 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998976, - 0.00436785, - 0.0450351, - 0.018658, - 0.866997, - -0.497963 - ], + "ImageOrientationPatientDICOM": [0.998976, 0.00436785, 0.0450351, 0.018658, 0.866997, -0.497963], "ImageOrientationText": "Tra>Cor(-29.9)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-02_ses-017_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 609, - -7197, - -8842, - 267, - 17, - -136, - -37, - 47 - ], + "ShimSetting": [609, -7197, -8842, 267, 17, -136, -37, 47], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_epi.json index e6821ac7a..4494482a9 100644 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998976, - 0.00436785, - 0.0450351, - 0.018658, - 0.866997, - -0.497963 - ], + "ImageOrientationPatientDICOM": [0.998976, 0.00436785, 0.0450351, 0.018658, 0.866997, -0.497963], "ImageOrientationText": "Tra>Cor(-29.9)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-02_ses-017_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 609, - -7197, - -8842, - 267, - 17, - -136, - -37, - 47 - ], + "ShimSetting": [609, -7197, -8842, 267, 17, -136, -37, 47], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_epi.json index a3b1934ff..5840cb28c 100644 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998976, - 0.00436785, - 0.0450351, - 0.018658, - 0.866997, - -0.497963 - ], + "ImageOrientationPatientDICOM": [0.998976, 0.00436785, 0.0450351, 0.018658, 0.866997, -0.497963], "ImageOrientationText": "Tra>Cor(-29.9)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-02_ses-017_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 609, - -7197, - -8842, - 267, - 17, - -136, - -37, - 47 - ], + "ShimSetting": [609, -7197, -8842, 267, 17, -136, -37, 47], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_epi.json index c0b198eda..d38ecc010 100644 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998976, - 0.00436785, - 0.0450351, - 0.018658, - 0.866997, - -0.497963 - ], + "ImageOrientationPatientDICOM": [0.998976, 0.00436785, 0.0450351, 0.018658, 0.866997, -0.497963], "ImageOrientationText": "Tra>Cor(-29.9)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-02_ses-017_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 609, - -7197, - -8842, - 267, - 17, - -136, - -37, - 47 - ], + "ShimSetting": [609, -7197, -8842, 267, 17, -136, -37, 47], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_epi.json index 24d04619b..cf90ee37c 100644 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998976, - 0.00436785, - 0.0450351, - 0.018658, - 0.866997, - -0.497963 - ], + "ImageOrientationPatientDICOM": [0.998976, 0.00436785, 0.0450351, 0.018658, 0.866997, -0.497963], "ImageOrientationText": "Tra>Cor(-29.9)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-02_ses-017_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 609, - -7197, - -8842, - 267, - 17, - -136, - -37, - 47 - ], + "ShimSetting": [609, -7197, -8842, 267, 17, -136, -37, 47], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_epi.json index 7498d3a84..4f2df0beb 100644 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_epi.json +++ b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-06_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998976, - 0.00436785, - 0.0450351, - 0.018658, - 0.866997, - -0.497963 - ], + "ImageOrientationPatientDICOM": [0.998976, 0.00436785, 0.0450351, 0.018658, 0.866997, -0.497963], "ImageOrientationText": "Tra>Cor(-29.9)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-02_ses-017_task-mario3_run-06_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-06_SBRef", "SeriesNumber": 24, - "ShimSetting": [ - 609, - -7197, - -8842, - 267, - 17, - -136, - -37, - 47 - ], + "ShimSetting": [609, -7197, -8842, 267, 17, -136, -37, 47], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_epi.json b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_epi.json index 414a3d250..3a742e897 100644 --- a/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_epi.json +++ b/sub-02/ses-017/fmap/sub-02_ses-017_acq-sbref_dir-PA_run-07_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998976, - 0.00436785, - 0.0450351, - 0.018658, - 0.866997, - -0.497963 - ], + "ImageOrientationPatientDICOM": [0.998976, 0.00436785, 0.0450351, 0.018658, 0.866997, -0.497963], "ImageOrientationText": "Tra>Cor(-29.9)>Sag(2.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-02_ses-017_task-mario3_run-07_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-07_SBRef", "SeriesNumber": 27, - "ShimSetting": [ - 609, - -7197, - -8842, - 267, - 17, - -136, - -37, - 47 - ], + "ShimSetting": [609, -7197, -8842, 267, 17, -136, -37, 47], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 1da15d57eea7c5624a050c6afc03307959b22dc6 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:20:09 -0400 Subject: [PATCH 317/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-06_ses-016_acq-axial_localizer.json | 81 +++ .../sub-06_ses-016_acq-axial_localizer.nii.gz | 1 + .../sub-06_ses-016_acq-coronal_localizer.json | 81 +++ ...ub-06_ses-016_acq-coronal_localizer.nii.gz | 1 + ...sub-06_ses-016_acq-sagittal_localizer.json | 86 +++ ...b-06_ses-016_acq-sagittal_localizer.nii.gz | 1 + sub-06/ses-016/anat/sub-06_ses-016_scout.json | 542 ++++++++++++++++++ .../ses-016/anat/sub-06_ses-016_scout.nii.gz | 1 + ...6_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-016_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...16_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...016_task-mario3_run-01_part-mag_events.tsv | 1 + ...016_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...16_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-01_part-phase_events.tsv | 1 + ...6_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-016_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...16_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...016_task-mario3_run-02_part-mag_events.tsv | 1 + ...016_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...16_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-02_part-phase_events.tsv | 1 + ...6_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-016_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...16_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...016_task-mario3_run-03_part-mag_events.tsv | 1 + ...016_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...16_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-03_part-phase_events.tsv | 1 + ...6_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-06/ses-016/sub-06_ses-016_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-06/ses-016/anat/sub-06_ses-016_acq-axial_localizer.json create mode 120000 sub-06/ses-016/anat/sub-06_ses-016_acq-axial_localizer.nii.gz create mode 100644 sub-06/ses-016/anat/sub-06_ses-016_acq-coronal_localizer.json create mode 120000 sub-06/ses-016/anat/sub-06_ses-016_acq-coronal_localizer.nii.gz create mode 100644 sub-06/ses-016/anat/sub-06_ses-016_acq-sagittal_localizer.json create mode 120000 sub-06/ses-016/anat/sub-06_ses-016_acq-sagittal_localizer.nii.gz create mode 100644 sub-06/ses-016/anat/sub-06_ses-016_scout.json create mode 120000 sub-06/ses-016/anat/sub-06_ses-016_scout.nii.gz create mode 100644 sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-06/ses-016/sub-06_ses-016_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 6f8f99e01..27e5c61cf 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 6f8f99e010561820978d008f26288602486558b0 +Subproject commit 27e5c61cff9d19927f5ca2fb39ba9459cbc48f31 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..db37a3f34 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-06 41 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-06/ses-016/anat/sub-06_ses-016_acq-axial_localizer.json b/sub-06/ses-016/anat/sub-06_ses-016_acq-axial_localizer.json new file mode 100644 index 000000000..5bfc16daf --- /dev/null +++ b/sub-06/ses-016/anat/sub-06_ses-016_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:50:20.325000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": 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newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..8d8944634 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.998497, -0.0505358, 0.0212311, 0.0547758, 0.93445, -0.351857], + 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17:20:54 -0400 Subject: [PATCH 318/463] fix fmap phase --- ...6_ses-014_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-014_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-014_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-014_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-014_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-014_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-014_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-06/ses-014/sub-06_ses-014_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-06/ses-014/fmap/{sub-06_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-06_ses-014_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-014/fmap/{sub-06_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-014_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-014/fmap/{sub-06_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-06_ses-014_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-014/fmap/{sub-06_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-014_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-014/fmap/{sub-06_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-06_ses-014_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-06/ses-014/fmap/{sub-06_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-06_ses-014_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-06/ses-014/fmap/{sub-06_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-06_ses-014_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-06/ses-014/fmap/{sub-06_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-06_ses-014_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-06/ses-014/fmap/{sub-06_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-06_ses-014_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-06/ses-014/fmap/{sub-06_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-06_ses-014_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 932e9056d..000000000 --- a/sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:21:15.307500", - "BandwidthPerPixelPhaseEncode": 17.17, - 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"SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999487222, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "161855.233000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["162115.307500", "162116.797500", "162118.287500"], - "ContentTime": ["162201.629000", "162201.631000", "162201.634000"], - "InstanceCreationTime": ["162201.629000", "162201.631000", "162201.634000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4760.0, 4756.0, 4754.0], - "WindowWidth": [18542.0, 18540.0, 18544.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 90b53a551..000000000 --- a/sub-06/ses-014/fmap/sub-06_ses-014_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/pQ/9x/MD5E-s3334832--2ad463e132d96ace5609a05f8f1f314f.nii.gz/MD5E-s3334832--2ad463e132d96ace5609a05f8f1f314f.nii.gz \ No newline at end of file diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 636a3d2a5..000000000 --- a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:21:4.877500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998198, - -0.0521176, - 0.0297528, - 0.0593039, - 0.932604, - -0.355996 - ], - "ImageOrientationText": "Tra>Cor(-20.9)>Sag(0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0379482, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 628, - -7249, - -8828, - 520, - 14, - -199, - -111, - 7 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 240.65, - "WipMemBlock": "4dd8cb82-1bde-4987-b854-3d10f36af66d||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 1e1a117b0..000000000 --- a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/xZ/W3/MD5E-s1112369--098bd826791368ee7a6c890897faed3f.nii.gz/MD5E-s1112369--098bd826791368ee7a6c890897faed3f.nii.gz \ No newline at end of file diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index c0938a0a5..000000000 --- a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:22:47.277500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998198, - -0.0521176, - 0.0297528, - 0.0593039, - 0.932604, - -0.355996 - ], - "ImageOrientationText": "Tra>Cor(-20.9)>Sag(0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0475837, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 628, - -7249, - -8828, - 520, - 14, - -199, - -111, - 7 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 240.65, - "WipMemBlock": "d494bb8d-57ab-45d4-a6c1-a8c2021dcec2||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index ed6b2462e..000000000 --- a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3G/pM/MD5E-s1103446--8a5aba677573ba787d1cd86d367738d4.nii.gz/MD5E-s1103446--8a5aba677573ba787d1cd86d367738d4.nii.gz \ No newline at end of file diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 2159da51c..000000000 --- a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:31:49.452500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998198, - -0.0521176, - 0.0297528, - 0.0593039, - 0.932604, - -0.355996 - ], - "ImageOrientationText": "Tra>Cor(-20.9)>Sag(0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0475837, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 628, - -7249, - -8828, - 520, - 14, - -199, - -111, - 7 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 240.65, - "WipMemBlock": "5489ddba-66b1-4bda-83be-326a7c3e643c||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 031c53918..000000000 --- a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/GX/JW/MD5E-s1103740--91fbc2ed2162ab56d89021873a34bec4.nii.gz/MD5E-s1103740--91fbc2ed2162ab56d89021873a34bec4.nii.gz \ No newline at end of file diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index ca963ab82..000000000 --- a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:41:37.947500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998198, - -0.0521176, - 0.0297528, - 0.0593039, - 0.932604, - -0.355996 - ], - "ImageOrientationText": "Tra>Cor(-20.9)>Sag(0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0475837, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 628, - -7249, - -8828, - 520, - 14, - -199, - -111, - 7 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 240.65, - "WipMemBlock": "81c647b0-8cb0-4796-815f-f3272cd118e3||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index ad4d691e4..000000000 --- a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/9f/J9/MD5E-s1103723--b05285ac059cb0f0d205ce62b1883e9f.nii.gz/MD5E-s1103723--b05285ac059cb0f0d205ce62b1883e9f.nii.gz \ No newline at end of file diff --git a/sub-06/ses-014/sub-06_ses-014_scans.tsv b/sub-06/ses-014/sub-06_ses-014_scans.tsv index 69eb7a779..d2584db99 120000 --- a/sub-06/ses-014/sub-06_ses-014_scans.tsv +++ b/sub-06/ses-014/sub-06_ses-014_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/9f/mZ/MD5E-s2667--a27c10164fc274c996636753c6a1dd33.tsv/MD5E-s2667--a27c10164fc274c996636753c6a1dd33.tsv \ No newline at end of file +../../.git/annex/objects/63/mf/MD5E-s2066--c03871c493019544439505b28520bf4f.tsv/MD5E-s2066--c03871c493019544439505b28520bf4f.tsv \ No newline at end of file From 8d224d300abb0306636722010574e7dc527c3bf1 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:20:58 -0400 Subject: [PATCH 319/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..c75148b72 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = bfb0e3c4-b8c0-48e0-a2da-47ec30f11d2f diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..12bca5c1c --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 12bca5c1c25e387b1515851fadf96d05d85c25cc From 5a8b5861bc9cd734b3215445600d2a6ed2527d49 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:21:06 -0400 Subject: [PATCH 320/463] fix fmap phase --- ...6_ses-016_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-016_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-016_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-016_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-016_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-016_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-016_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-06/ses-016/sub-06_ses-016_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-06/ses-016/fmap/{sub-06_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-06_ses-016_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-016/fmap/{sub-06_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-016_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-016/fmap/{sub-06_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-06_ses-016_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-016/fmap/{sub-06_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-016_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-016/fmap/{sub-06_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-06_ses-016_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-06/ses-016/fmap/{sub-06_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-06_ses-016_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-06/ses-016/fmap/{sub-06_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-06_ses-016_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-06/ses-016/fmap/{sub-06_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-06_ses-016_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-06/ses-016/fmap/{sub-06_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-06_ses-016_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-06/ses-016/fmap/{sub-06_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-06_ses-016_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 32d6c14a7..000000000 --- a/sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:51:21.885000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.998497, -0.0505358, 0.0212311, 0.0547758, 0.93445, -0.351857], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0364229, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [613, -7268, -8824, 521, 2, -196, -83, 9], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.0975, 0.8825, 0.195, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685, 0, 0.785, 0.0975, 0.8825, 0.195, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685, 0, 0.785, 0.0975, 0.8825, 0.195, 0.98, 0.295, 1.0775, 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"slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["155121.885000", "155123.375000", "155124.865000"], - "ContentTime": ["155207.959000", "155207.961000", "155207.964000"], - "InstanceCreationTime": ["155207.959000", "155207.961000", "155207.964000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4734.0, 4708.0, 4712.0], - "WindowWidth": [18548.0, 18510.0, 18520.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 94d248692..000000000 --- a/sub-06/ses-016/fmap/sub-06_ses-016_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Z6/7x/MD5E-s3334202--2e108694dc0809442f1b677ddb4c18a7.nii.gz/MD5E-s3334202--2e108694dc0809442f1b677ddb4c18a7.nii.gz \ No newline at end of file diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 67b8de4e0..000000000 --- a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:51:11.455000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998497, - -0.0505358, - 0.0212311, - 0.0547758, - 0.93445, - -0.351857 - ], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0364229, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 613, - -7268, - -8824, - 521, - 2, - -196, - -83, - 9 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": 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sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 85eae63c5..000000000 --- a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:52:42.780000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998497, - -0.0505358, - 0.0212311, - 0.0547758, - 0.93445, - -0.351857 - ], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0456711, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 613, - -7268, - -8824, - 521, - 2, - -196, - -83, - 9 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 233.77, - "WipMemBlock": "931ed7e6-7aed-48dc-917d-45189509e0a9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 98bf73ee3..000000000 --- a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/FQ/92/MD5E-s1103559--152d22c3bce9421894473a18bf1ce559.nii.gz/MD5E-s1103559--152d22c3bce9421894473a18bf1ce559.nii.gz \ No newline at end of file diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 5d3b30034..000000000 --- a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:01:16.752500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - 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1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 233.77, - "WipMemBlock": "66039221-ed63-4c6c-92ce-287149c829b5||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index bed1953a5..000000000 --- a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/gK/jZ/MD5E-s1103397--0d66772abb493d60648cc0f85b98aa77.nii.gz/MD5E-s1103397--0d66772abb493d60648cc0f85b98aa77.nii.gz \ No newline at end of file diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 5cfdaaa9a..000000000 --- a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:10:21.097500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998497, - -0.0505358, - 0.0212311, - 0.0547758, - 0.93445, - -0.351857 - ], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0456711, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 613, - -7268, - -8824, - 521, - 2, - -196, - -83, - 9 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 233.77, - "WipMemBlock": "dc95c1f5-77f9-4506-bbcf-afe8efa636d1||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index e6ba8d4e0..000000000 --- a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/wK/x9/MD5E-s1103514--f89a66fc3b05dcb254d46744ab6cabf2.nii.gz/MD5E-s1103514--f89a66fc3b05dcb254d46744ab6cabf2.nii.gz \ No newline at end of file diff --git a/sub-06/ses-016/sub-06_ses-016_scans.tsv b/sub-06/ses-016/sub-06_ses-016_scans.tsv index e46021d90..f9f4674b0 120000 --- a/sub-06/ses-016/sub-06_ses-016_scans.tsv +++ b/sub-06/ses-016/sub-06_ses-016_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/Gz/X0/MD5E-s2667--88413d2a3236ab1b13921e62e2a5a74b.tsv/MD5E-s2667--88413d2a3236ab1b13921e62e2a5a74b.tsv \ No newline at end of file +../../.git/annex/objects/z7/fx/MD5E-s2066--095978ac1b84f5dceeef5f7a1455f89f.tsv/MD5E-s2066--095978ac1b84f5dceeef5f7a1455f89f.tsv \ No newline at end of file From b651a95be75be4f23b77c3eb9346062d5ca5218d Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:21:08 -0400 Subject: [PATCH 321/463] fix complex event files --- ...g_events.tsv => sub-06_ses-014_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-06_ses-014_task-mario3_run-02_events.tsv} | 0 .../func/sub-06_ses-014_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-06_ses-014_task-mario3_run-03_events.tsv} | 0 .../func/sub-06_ses-014_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-06_ses-014_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-06/ses-014/func/{sub-06_ses-014_task-mario3_run-01_part-mag_events.tsv => sub-06_ses-014_task-mario3_run-01_events.tsv} (100%) rename sub-06/ses-014/func/{sub-06_ses-014_task-mario3_run-01_part-phase_events.tsv => sub-06_ses-014_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-02_part-phase_events.tsv rename sub-06/ses-014/func/{sub-06_ses-014_task-mario3_run-02_part-mag_events.tsv => sub-06_ses-014_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-01_part-mag_events.tsv b/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-01_events.tsv similarity index 100% rename from sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-01_part-mag_events.tsv rename to sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-01_events.tsv diff --git a/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-01_part-phase_events.tsv b/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-02_events.tsv similarity index 100% rename from sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-01_part-phase_events.tsv rename to sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-02_events.tsv diff --git a/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-02_part-phase_events.tsv b/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-02_part-mag_events.tsv b/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_events.tsv similarity index 100% rename from sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-02_part-mag_events.tsv rename to sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_events.tsv diff --git a/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_part-mag_events.tsv b/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_part-phase_events.tsv b/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-014/func/sub-06_ses-014_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From b6976df1bc0dc29e9fd501624842cbee4634fe87 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:21:20 -0400 Subject: [PATCH 322/463] fix complex event files --- ...g_events.tsv => sub-06_ses-016_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-06_ses-016_task-mario3_run-02_events.tsv} | 0 .../func/sub-06_ses-016_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-06_ses-016_task-mario3_run-03_events.tsv} | 0 .../func/sub-06_ses-016_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-06_ses-016_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-06/ses-016/func/{sub-06_ses-016_task-mario3_run-01_part-mag_events.tsv => sub-06_ses-016_task-mario3_run-01_events.tsv} (100%) rename sub-06/ses-016/func/{sub-06_ses-016_task-mario3_run-01_part-phase_events.tsv => sub-06_ses-016_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-02_part-phase_events.tsv rename sub-06/ses-016/func/{sub-06_ses-016_task-mario3_run-02_part-mag_events.tsv => sub-06_ses-016_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-01_part-mag_events.tsv b/sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-01_events.tsv similarity index 100% rename from sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-01_part-mag_events.tsv rename to sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-01_events.tsv diff --git a/sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-01_part-phase_events.tsv b/sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-02_events.tsv similarity index 100% rename from sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-01_part-phase_events.tsv rename to sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-02_events.tsv diff --git a/sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-02_part-phase_events.tsv b/sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-02_part-mag_events.tsv b/sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_events.tsv similarity index 100% rename from sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-02_part-mag_events.tsv rename to sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_events.tsv diff --git a/sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_part-mag_events.tsv b/sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_part-phase_events.tsv b/sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-016/func/sub-06_ses-016_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From b4310a2a094e622948ef8b265b67e0b59bbf5732 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:21:36 -0400 Subject: [PATCH 323/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..2b5635916 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = aa2003ce-3059-4465-952c-07cbfcb47d9c diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..a0a403ba6 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit a0a403ba6db82ec20684e760b86025e1368e3d9b From 7be8fa8edaa40c10af983b43fb81505f355e1c94 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:21:52 -0400 Subject: [PATCH 324/463] fill IntendedFor --- ...6_ses-014_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...6_ses-014_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...6_ses-014_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...6_ses-014_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_epi.json b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_epi.json index 97f9b0fb6..f0a956ee1 100644 --- a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998198, - -0.0521176, - 0.0297528, - 0.0593039, - 0.932604, - -0.355996 - ], + "ImageOrientationPatientDICOM": [0.998198, -0.0521176, 0.0297528, 0.0593039, 0.932604, -0.355996], "ImageOrientationText": "Tra>Cor(-20.9)>Sag(0.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-06_ses-014_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-014/func/sub-06_ses-014_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-014/func/sub-06_ses-014_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 628, - -7249, - -8828, - 520, - 14, - -199, - -111, - 7 - ], + "ShimSetting": [628, -7249, -8828, 520, 14, -199, -111, 7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_epi.json b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_epi.json index c177d5f61..834d78464 100644 --- a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998198, - -0.0521176, - 0.0297528, - 0.0593039, - 0.932604, - -0.355996 - ], + "ImageOrientationPatientDICOM": [0.998198, -0.0521176, 0.0297528, 0.0593039, 0.932604, -0.355996], "ImageOrientationText": "Tra>Cor(-20.9)>Sag(0.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-06_ses-014_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 628, - -7249, - -8828, - 520, - 14, - -199, - -111, - 7 - ], + "ShimSetting": [628, -7249, -8828, 520, 14, -199, -111, 7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_epi.json b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_epi.json index 77517cefa..803c80e9c 100644 --- a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998198, - -0.0521176, - 0.0297528, - 0.0593039, - 0.932604, - -0.355996 - ], + "ImageOrientationPatientDICOM": [0.998198, -0.0521176, 0.0297528, 0.0593039, 0.932604, -0.355996], "ImageOrientationText": "Tra>Cor(-20.9)>Sag(0.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-06_ses-014_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 628, - -7249, - -8828, - 520, - 14, - -199, - -111, - 7 - ], + "ShimSetting": [628, -7249, -8828, 520, 14, -199, -111, 7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_epi.json b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_epi.json index 585e9a445..90f334c24 100644 --- a/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-06/ses-014/fmap/sub-06_ses-014_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998198, - -0.0521176, - 0.0297528, - 0.0593039, - 0.932604, - -0.355996 - ], + "ImageOrientationPatientDICOM": [0.998198, -0.0521176, 0.0297528, 0.0593039, 0.932604, -0.355996], "ImageOrientationText": "Tra>Cor(-20.9)>Sag(0.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-014/func/sub-06_ses-014_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 628, - -7249, - -8828, - 520, - 14, - -199, - -111, - 7 - ], + "ShimSetting": [628, -7249, -8828, 520, 14, -199, -111, 7], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 6e76535a64cc4947fc52b9af956d5026a2679ff1 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:22:26 -0400 Subject: [PATCH 325/463] fill IntendedFor --- ...6_ses-016_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...6_ses-016_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...6_ses-016_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...6_ses-016_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_epi.json b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_epi.json index 2e122e733..83df79030 100644 --- a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998497, - -0.0505358, - 0.0212311, - 0.0547758, - 0.93445, - -0.351857 - ], + "ImageOrientationPatientDICOM": [0.998497, -0.0505358, 0.0212311, 0.0547758, 0.93445, -0.351857], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-06_ses-016_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-016/func/sub-06_ses-016_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-016/func/sub-06_ses-016_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 613, - -7268, - -8824, - 521, - 2, - -196, - -83, - 9 - ], + "ShimSetting": [613, -7268, -8824, 521, 2, -196, -83, 9], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_epi.json b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_epi.json index ff63a5fa3..ea5d395ed 100644 --- a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998497, - -0.0505358, - 0.0212311, - 0.0547758, - 0.93445, - -0.351857 - ], + "ImageOrientationPatientDICOM": [0.998497, -0.0505358, 0.0212311, 0.0547758, 0.93445, -0.351857], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-06_ses-016_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 613, - -7268, - -8824, - 521, - 2, - -196, - -83, - 9 - ], + "ShimSetting": [613, -7268, -8824, 521, 2, -196, -83, 9], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_epi.json b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_epi.json index dbd59b7af..78c175675 100644 --- a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998497, - -0.0505358, - 0.0212311, - 0.0547758, - 0.93445, - -0.351857 - ], + "ImageOrientationPatientDICOM": [0.998497, -0.0505358, 0.0212311, 0.0547758, 0.93445, -0.351857], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-06_ses-016_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 613, - -7268, - -8824, - 521, - 2, - -196, - -83, - 9 - ], + "ShimSetting": [613, -7268, -8824, 521, 2, -196, -83, 9], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_epi.json b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_epi.json index 81c0eb9fb..c8c08cdba 100644 --- a/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-06/ses-016/fmap/sub-06_ses-016_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998497, - -0.0505358, - 0.0212311, - 0.0547758, - 0.93445, - -0.351857 - ], + "ImageOrientationPatientDICOM": [0.998497, -0.0505358, 0.0212311, 0.0547758, 0.93445, -0.351857], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-016/func/sub-06_ses-016_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 613, - -7268, - -8824, - 521, - 2, - -196, - -83, - 9 - ], + "ShimSetting": [613, -7268, -8824, 521, 2, -196, -83, 9], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 7c63115f3130ad1574afb22625fa472673b5c172 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:23:00 -0400 Subject: [PATCH 326/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..b5a859d99 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 6b251026-f480-4743-b00e-48540f48ca74 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..236040bca --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 236040bca803cfa9b762ee95efb9d66ef38d46f5 From 9f4a3cbc8b1ffd909c004d0a740fca34fe5f46d1 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:23:24 -0400 Subject: [PATCH 327/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-03_ses-017_acq-axial_localizer.json | 81 +++ .../sub-03_ses-017_acq-axial_localizer.nii.gz | 1 + .../sub-03_ses-017_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-017_acq-coronal_localizer.nii.gz | 1 + ...sub-03_ses-017_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-017_acq-sagittal_localizer.nii.gz | 1 + sub-03/ses-017/anat/sub-03_ses-017_scout.json | 542 ++++++++++++++++++ .../ses-017/anat/sub-03_ses-017_scout.nii.gz | 1 + ...7_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ...-017_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...017_task-mario3_run-01_part-mag_events.tsv | 1 + ...017_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-01_part-phase_events.tsv | 1 + ...7_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-017_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...017_task-mario3_run-02_part-mag_events.tsv | 1 + ...017_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-02_part-phase_events.tsv | 1 + ...7_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-017_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...017_task-mario3_run-03_part-mag_events.tsv | 1 + ...017_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-03_part-phase_events.tsv | 1 + ...7_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-017_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...017_task-mario3_run-04_part-mag_events.tsv | 1 + ...017_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-04_part-phase_events.tsv | 1 + ...7_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-017_task-mario3_run-05_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...017_task-mario3_run-05_part-mag_events.tsv | 1 + ...017_task-mario3_run-05_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-05_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-05_part-phase_events.tsv | 1 + ...7_task-mario3_run-05_part-phase_sbref.json | 153 +++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + sub-03/ses-017/sub-03_ses-017_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 93 files changed, 6371 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-017/anat/sub-03_ses-017_acq-axial_localizer.json create mode 120000 sub-03/ses-017/anat/sub-03_ses-017_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-017/anat/sub-03_ses-017_acq-coronal_localizer.json create mode 120000 sub-03/ses-017/anat/sub-03_ses-017_acq-coronal_localizer.nii.gz create mode 100644 sub-03/ses-017/anat/sub-03_ses-017_acq-sagittal_localizer.json create mode 120000 sub-03/ses-017/anat/sub-03_ses-017_acq-sagittal_localizer.nii.gz create mode 100644 sub-03/ses-017/anat/sub-03_ses-017_scout.json create mode 120000 sub-03/ses-017/anat/sub-03_ses-017_scout.nii.gz create mode 100644 sub-03/ses-017/fmap/sub-03_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-017/fmap/sub-03_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-017/fmap/sub-03_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-017/fmap/sub-03_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 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160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit a0a403ba6db82ec20684e760b86025e1368e3d9b +Subproject commit 88e42de960cae5a276c0732fe2f2338298710bb9 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-03/ses-017/anat/sub-03_ses-017_acq-axial_localizer.json b/sub-03/ses-017/anat/sub-03_ses-017_acq-axial_localizer.json new file mode 100644 index 000000000..373812e46 --- /dev/null +++ b/sub-03/ses-017/anat/sub-03_ses-017_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:44:49.095000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": 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b/sub-03/ses-017/anat/sub-03_ses-017_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:44:56.085000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, 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"SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 229.914 +} \ No newline at end of file diff --git a/sub-03/ses-017/anat/sub-03_ses-017_acq-coronal_localizer.nii.gz b/sub-03/ses-017/anat/sub-03_ses-017_acq-coronal_localizer.nii.gz new file mode 120000 index 000000000..5858ff3bf --- /dev/null +++ b/sub-03/ses-017/anat/sub-03_ses-017_acq-coronal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/0P/KM/MD5E-s182224--0e5ac350ece49cc69cb3c5522ce85aee.nii.gz/MD5E-s182224--0e5ac350ece49cc69cb3c5522ce85aee.nii.gz \ No newline at end of file diff --git a/sub-03/ses-017/anat/sub-03_ses-017_acq-sagittal_localizer.json b/sub-03/ses-017/anat/sub-03_ses-017_acq-sagittal_localizer.json new file mode 100644 index 000000000..a57ee9b61 --- /dev/null +++ b/sub-03/ses-017/anat/sub-03_ses-017_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:44:42.105000", + "BaseResolution": 256, + 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a/sub-03/ses-017/anat/sub-03_ses-017_acq-sagittal_localizer.nii.gz b/sub-03/ses-017/anat/sub-03_ses-017_acq-sagittal_localizer.nii.gz new file mode 120000 index 000000000..307236459 --- /dev/null +++ b/sub-03/ses-017/anat/sub-03_ses-017_acq-sagittal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Z0/54/MD5E-s582936--51e8a88e3ce35e9cbc9b23f06d1218a8.nii.gz/MD5E-s582936--51e8a88e3ce35e9cbc9b23f06d1218a8.nii.gz \ No newline at end of file diff --git a/sub-03/ses-017/anat/sub-03_ses-017_scout.json b/sub-03/ses-017/anat/sub-03_ses-017_scout.json new file mode 100644 index 000000000..3da197505 --- /dev/null +++ b/sub-03/ses-017/anat/sub-03_ses-017_scout.json @@ -0,0 +1,542 @@ +{ + "AcquisitionMatrixPE": 160, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:44:26.682500", + "BaseResolution": 160, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + 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a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-05_part-phase_sbref.nii.gz b/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-05_part-phase_sbref.nii.gz new file mode 120000 index 000000000..5b6c00152 --- /dev/null +++ b/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-05_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/M3/fx/MD5E-s1103727--30bdbd6fea31f62a7171b052ec25b026.nii.gz/MD5E-s1103727--30bdbd6fea31f62a7171b052ec25b026.nii.gz \ No newline at end of file diff --git a/sub-03/ses-017/sub-03_ses-017_scans.tsv b/sub-03/ses-017/sub-03_ses-017_scans.tsv new file mode 120000 index 000000000..a84efc78f --- /dev/null +++ b/sub-03/ses-017/sub-03_ses-017_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/gK/fx/MD5E-s3911--791edf59faa440924bfd167830a3b60a.tsv/MD5E-s3911--791edf59faa440924bfd167830a3b60a.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..98e50681b --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999979, 0.00617039, -0.00191991, -0.00645766, 0.965269, -0.261178], + "ImageOrientationText": "Tra>Cor(-15.1)>Sag(-0.0)", + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0581824, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [613, -7226, -8776, 686, 62, -75, 64, -10], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 229.914, + "dcmmeta_affine": [ + [-1.9999582767486572, -0.012915311381220818, -0.0004833295533899218, 109.35244750976562], + [-0.012340771034359932, 1.930538296699524, -0.5223693251609802, -73.38195037841797], + [-0.003839824115857482, 0.5223554372787476, 1.9305776357650757, -57.357330322265625], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From abc7d9ff6daa127463ef3fb4643fefab10000067 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:23:50 -0400 Subject: [PATCH 328/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..976320e44 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 71add8b5-f85f-47af-a797-ac5d92ae16b8 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..62adb1701 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 62adb17012750b54076966ab866d1e1670b074a2 From 0ee4586ec2ed6e0846536448aa535a8528aadbd0 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:24:11 -0400 Subject: [PATCH 329/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-06_ses-018_acq-axial_localizer.json | 81 +++ .../sub-06_ses-018_acq-axial_localizer.nii.gz | 1 + .../sub-06_ses-018_acq-coronal_localizer.json | 81 +++ ...ub-06_ses-018_acq-coronal_localizer.nii.gz | 1 + ...sub-06_ses-018_acq-sagittal_localizer.json | 86 +++ ...b-06_ses-018_acq-sagittal_localizer.nii.gz | 1 + sub-06/ses-018/anat/sub-06_ses-018_scout.json | 542 ++++++++++++++++++ .../ses-018/anat/sub-06_ses-018_scout.nii.gz | 1 + ...8_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-018_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...18_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...018_task-mario3_run-01_part-mag_events.tsv | 1 + ...018_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...18_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-01_part-phase_events.tsv | 1 + ...8_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-018_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...18_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...018_task-mario3_run-02_part-mag_events.tsv | 1 + ...018_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...18_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-02_part-phase_events.tsv | 1 + ...8_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-018_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...18_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...018_task-mario3_run-03_part-mag_events.tsv | 1 + ...018_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...18_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-03_part-phase_events.tsv | 1 + ...8_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-06/ses-018/sub-06_ses-018_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-06/ses-018/anat/sub-06_ses-018_acq-axial_localizer.json create mode 120000 sub-06/ses-018/anat/sub-06_ses-018_acq-axial_localizer.nii.gz create mode 100644 sub-06/ses-018/anat/sub-06_ses-018_acq-coronal_localizer.json create mode 120000 sub-06/ses-018/anat/sub-06_ses-018_acq-coronal_localizer.nii.gz create mode 100644 sub-06/ses-018/anat/sub-06_ses-018_acq-sagittal_localizer.json create mode 120000 sub-06/ses-018/anat/sub-06_ses-018_acq-sagittal_localizer.nii.gz create mode 100644 sub-06/ses-018/anat/sub-06_ses-018_scout.json create mode 120000 sub-06/ses-018/anat/sub-06_ses-018_scout.nii.gz create mode 100644 sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-06/ses-018/sub-06_ses-018_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 236040bca..3e967b6f9 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 236040bca803cfa9b762ee95efb9d66ef38d46f5 +Subproject commit 3e967b6f95eae0b884f83f3544b6f6f5ae0e14a4 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..db37a3f34 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-06 41 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-06/ses-018/anat/sub-06_ses-018_acq-axial_localizer.json b/sub-06/ses-018/anat/sub-06_ses-018_acq-axial_localizer.json new file mode 100644 index 000000000..65b1b3b4b --- /dev/null +++ b/sub-06/ses-018/anat/sub-06_ses-018_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:58:41.040000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + 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"981c642b-80bf-49ef-bd3d-faf02de93db9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-phase_sbref.nii.gz b/sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-phase_sbref.nii.gz new file mode 120000 index 000000000..148f95f98 --- /dev/null +++ b/sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/VF/MK/MD5E-s1103765--30071e456e76a088d95ed715202bacd8.nii.gz/MD5E-s1103765--30071e456e76a088d95ed715202bacd8.nii.gz \ No newline at end of file diff --git a/sub-06/ses-018/sub-06_ses-018_scans.tsv b/sub-06/ses-018/sub-06_ses-018_scans.tsv new file mode 120000 index 000000000..39a21f2d8 --- /dev/null +++ b/sub-06/ses-018/sub-06_ses-018_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/1z/kv/MD5E-s2660--33b5e0496b215e9da0d9e599112605fa.tsv/MD5E-s2660--33b5e0496b215e9da0d9e599112605fa.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..f4806a40d --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999261, -0.0333538, 0.0191044, 0.0378637, 0.939719, -0.339846], + "ImageOrientationText": "Tra>Cor(-19.9)>Sag(0.4)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.055255, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [589, -7288, -8814, 517, 42, -287, -163, 57], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 241.173, + "dcmmeta_affine": [ + [-1.9985220432281494, 0.07572740316390991, 0.013235163874924183, 103.80171966552734], + [0.06670759618282318, 1.8794374465942383, -0.6806355714797974, -68.4758071899414], + [0.03820871561765671, 0.6796911358833313, 1.8805744647979736, -64.08352661132812], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 146dc068855d97aab99e4d93b25ad4aca037fd5f Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:24:53 -0400 Subject: [PATCH 330/463] fix fmap phase --- ...3_ses-017_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-017_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-017_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - sub-03/ses-017/sub-03_ses-017_scans.tsv | 2 +- 29 files changed, 1 insertion(+), 1097 deletions(-) rename sub-03/ses-017/fmap/{sub-03_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-017_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-017/fmap/{sub-03_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-017_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-017/fmap/sub-03_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-017/fmap/sub-03_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-017/fmap/{sub-03_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-017_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-017/fmap/{sub-03_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-017_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-017/fmap/{sub-03_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-017_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-017/fmap/{sub-03_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-017_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-017/fmap/{sub-03_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-017_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-017/fmap/{sub-03_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-017_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-03/ses-017/fmap/{sub-03_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-03_ses-017_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-03/ses-017/fmap/{sub-03_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-03_ses-017_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-03/ses-017/fmap/{sub-03_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-03_ses-017_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-03/ses-017/fmap/{sub-03_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-03_ses-017_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-03/ses-017/fmap/{sub-03_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-03_ses-017_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-03/ses-017/fmap/{sub-03_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-03_ses-017_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-017/fmap/sub-03_ses-017_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-017/fmap/sub-03_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-017/fmap/sub-03_ses-017_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-017/fmap/sub-03_ses-017_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-017/fmap/sub-03_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-017/fmap/sub-03_ses-017_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-017/fmap/sub-03_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 6c73b855a..000000000 --- a/sub-03/ses-017/fmap/sub-03_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:45:52.825000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999979, 0.00617039, -0.00191991, -0.00645766, 0.965269, -0.261178], - "ImageOrientationText": "Tra>Cor(-15.1)>Sag(-0.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0464007, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [613, -7226, -8776, 686, 62, -75, 64, -10], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.6875], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.914, - "WipMemBlock": "be0f8fa5-14b7-4d97-8563-5fdf6d852ec8||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9999582767486572, -0.012915311381220818, -0.0004833295533899218, 109.35244750976562], - [-0.012340771034359932, 1.930538296699524, -0.5223693251609802, -73.38195037841797], - [-0.003839824115857482, 0.5223554372787476, 1.9305776357650757, -57.357330322265625], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - 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sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 2f7cdf629..000000000 --- a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:45:42.395000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999979, - 0.00617039, - -0.00191991, - -0.00645766, - 0.965269, - -0.261178 - ], - "ImageOrientationText": "Tra>Cor(-15.1)>Sag(-0.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0464007, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 613, - -7226, - -8776, - 686, - 62, - -75, - 64, - -10 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.914, - "WipMemBlock": "be0f8fa5-14b7-4d97-8563-5fdf6d852ec8||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 30f6aecba..000000000 --- a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/J6/wm/MD5E-s1112195--bee8f94b2809370f125a6f44de35e50e.nii.gz/MD5E-s1112195--bee8f94b2809370f125a6f44de35e50e.nii.gz \ No newline at end of file diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 6cb84cb92..000000000 --- a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:47:22.360000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999979, - 0.00617039, - -0.00191991, - -0.00645766, - 0.965269, - -0.261178 - ], - "ImageOrientationText": "Tra>Cor(-15.1)>Sag(-0.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", 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1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.914, - "WipMemBlock": "b3719347-1300-4cf0-941c-66ac0a5bb80e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 20de0e510..000000000 --- a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/G5/9z/MD5E-s1103720--05d5cc8fcd1673b8517b7516291b3249.nii.gz/MD5E-s1103720--05d5cc8fcd1673b8517b7516291b3249.nii.gz \ No newline at end of file diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index d3f74b9d4..000000000 --- a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:01:39.255000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": 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"games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0581824, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 613, - -7226, - -8776, - 686, - 62, - -75, - 64, - -10 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.914, - "WipMemBlock": "13f4b991-790e-48ed-a0bc-6da35a84ad66||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 935e3b6c9..000000000 --- a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/jX/91/MD5E-s1103855--bd7d10fe309d9fb68c9ac9ba84a22bcc.nii.gz/MD5E-s1103855--bd7d10fe309d9fb68c9ac9ba84a22bcc.nii.gz \ No newline at end of file diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 1e2193817..000000000 --- a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:12:6.780000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999979, - 0.00617039, - -0.00191991, - -0.00645766, - 0.965269, - -0.261178 - ], - "ImageOrientationText": "Tra>Cor(-15.1)>Sag(-0.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - 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sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 5e110548d..000000000 --- a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:21:20.755000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999979, - 0.00617039, - -0.00191991, - -0.00645766, - 0.965269, - -0.261178 - ], - "ImageOrientationText": "Tra>Cor(-15.1)>Sag(-0.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0581824, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 613, - -7226, - -8776, - 686, - 62, - -75, - 64, - -10 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.914, - "WipMemBlock": "14e1e246-e5f2-46e0-ad8c-8514eb8dba61||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 8956fc20b..000000000 --- a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/27/mF/MD5E-s1103500--740decbef967fe5ad1b13766ea6ee4f4.nii.gz/MD5E-s1103500--740decbef967fe5ad1b13766ea6ee4f4.nii.gz \ No newline at end of file diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index a50b7f158..000000000 --- a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:31:24.002500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999979, - 0.00617039, - -0.00191991, - -0.00645766, - 0.965269, - -0.261178 - ], - "ImageOrientationText": "Tra>Cor(-15.1)>Sag(-0.0)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-05", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0581824, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 613, - -7226, - -8776, - 686, - 62, - -75, - 64, - -10 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.914, - "WipMemBlock": "e0b5f078-3458-4c96-8c86-eb98c1d82742||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index 5b6c00152..000000000 --- a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/M3/fx/MD5E-s1103727--30bdbd6fea31f62a7171b052ec25b026.nii.gz/MD5E-s1103727--30bdbd6fea31f62a7171b052ec25b026.nii.gz \ No newline at end of file diff --git a/sub-03/ses-017/sub-03_ses-017_scans.tsv b/sub-03/ses-017/sub-03_ses-017_scans.tsv index a84efc78f..b9984fabb 120000 --- a/sub-03/ses-017/sub-03_ses-017_scans.tsv +++ b/sub-03/ses-017/sub-03_ses-017_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/gK/fx/MD5E-s3911--791edf59faa440924bfd167830a3b60a.tsv/MD5E-s3911--791edf59faa440924bfd167830a3b60a.tsv \ No newline at end of file +../../.git/annex/objects/xw/93/MD5E-s3068--31cc75ab0f49285d537c2fbbce06f484.tsv/MD5E-s3068--31cc75ab0f49285d537c2fbbce06f484.tsv \ No newline at end of file From 1fde191049681266274c4af6187d8b9053261ca5 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:24:56 -0400 Subject: [PATCH 331/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-06_ses-012_acq-axial_localizer.json | 81 +++ .../sub-06_ses-012_acq-axial_localizer.nii.gz | 1 + .../sub-06_ses-012_acq-coronal_localizer.json | 81 +++ ...ub-06_ses-012_acq-coronal_localizer.nii.gz | 1 + ...sub-06_ses-012_acq-sagittal_localizer.json | 86 +++ ...b-06_ses-012_acq-sagittal_localizer.nii.gz | 1 + sub-06/ses-012/anat/sub-06_ses-012_scout.json | 542 ++++++++++++++++++ .../ses-012/anat/sub-06_ses-012_scout.nii.gz | 1 + ...2_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-012_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...12_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...012_task-mario3_run-01_part-mag_events.tsv | 1 + ...012_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...12_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-01_part-phase_events.tsv | 1 + ...2_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-012_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...12_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...012_task-mario3_run-02_part-mag_events.tsv | 1 + ...012_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...12_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-02_part-phase_events.tsv | 1 + ...2_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-012_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...12_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...012_task-mario3_run-03_part-mag_events.tsv | 1 + ...012_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...12_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-03_part-phase_events.tsv | 1 + ...2_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-06/ses-012/sub-06_ses-012_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-06/ses-012/anat/sub-06_ses-012_acq-axial_localizer.json create mode 120000 sub-06/ses-012/anat/sub-06_ses-012_acq-axial_localizer.nii.gz create mode 100644 sub-06/ses-012/anat/sub-06_ses-012_acq-coronal_localizer.json create mode 120000 sub-06/ses-012/anat/sub-06_ses-012_acq-coronal_localizer.nii.gz create mode 100644 sub-06/ses-012/anat/sub-06_ses-012_acq-sagittal_localizer.json create mode 120000 sub-06/ses-012/anat/sub-06_ses-012_acq-sagittal_localizer.nii.gz create mode 100644 sub-06/ses-012/anat/sub-06_ses-012_scout.json create mode 120000 sub-06/ses-012/anat/sub-06_ses-012_scout.nii.gz create mode 100644 sub-06/ses-012/fmap/sub-06_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-012/fmap/sub-06_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-012/fmap/sub-06_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-012/fmap/sub-06_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-06/ses-012/sub-06_ses-012_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 62adb1701..b0e604089 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 62adb17012750b54076966ab866d1e1670b074a2 +Subproject commit b0e6040895a6c32987b37b33a863e69f873d62e9 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..db37a3f34 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-06 41 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-06/ses-012/anat/sub-06_ses-012_acq-axial_localizer.json b/sub-06/ses-012/anat/sub-06_ses-012_acq-axial_localizer.json new file mode 100644 index 000000000..4e0b24ea8 --- /dev/null +++ b/sub-06/ses-012/anat/sub-06_ses-012_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:17:48.060000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0280622, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 229.674 +} \ No newline at end of file diff --git a/sub-06/ses-012/anat/sub-06_ses-012_acq-axial_localizer.nii.gz b/sub-06/ses-012/anat/sub-06_ses-012_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..4b2a2d217 --- /dev/null +++ b/sub-06/ses-012/anat/sub-06_ses-012_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Vp/P5/MD5E-s167719--ed6f44d7f137db57da2e84977d129a07.nii.gz/MD5E-s167719--ed6f44d7f137db57da2e84977d129a07.nii.gz \ No newline at end of file diff --git a/sub-06/ses-012/anat/sub-06_ses-012_acq-coronal_localizer.json b/sub-06/ses-012/anat/sub-06_ses-012_acq-coronal_localizer.json new file mode 100644 index 000000000..c33d91e5c --- /dev/null +++ b/sub-06/ses-012/anat/sub-06_ses-012_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:17:55.050000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": 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a/sub-06/ses-012/anat/sub-06_ses-012_acq-sagittal_localizer.json b/sub-06/ses-012/anat/sub-06_ses-012_acq-sagittal_localizer.json new file mode 100644 index 000000000..43ae59190 --- /dev/null +++ b/sub-06/ses-012/anat/sub-06_ses-012_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:17:41.070000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 0, + 1, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Sag", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + 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"fa6b0374-01e0-4074-a3f2-8ec13743ade9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-phase_sbref.nii.gz b/sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-phase_sbref.nii.gz new file mode 120000 index 000000000..e01543e2f --- /dev/null +++ b/sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Jx/kF/MD5E-s1103729--5479eeb4325cbd4b9da96e268d344fa5.nii.gz/MD5E-s1103729--5479eeb4325cbd4b9da96e268d344fa5.nii.gz \ No newline at end of file diff --git a/sub-06/ses-012/sub-06_ses-012_scans.tsv b/sub-06/ses-012/sub-06_ses-012_scans.tsv new file mode 120000 index 000000000..e9012f9a9 --- /dev/null +++ b/sub-06/ses-012/sub-06_ses-012_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/98/Xx/MD5E-s2667--f5a1d35ec63c70dc9885b1132fa4898b.tsv/MD5E-s2667--f5a1d35ec63c70dc9885b1132fa4898b.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..227c426ff --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.998837, -0.0477724, 0.00653306, 0.0471039, 0.937835, -0.343869], + "ImageOrientationText": "Tra>Cor(-20.1)>Sag(-0.6)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0413329, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [624, -7262, -8829, 527, 23, -242, -78, -15], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 229.674, + "dcmmeta_affine": [ + [-1.997673749923706, 0.09420786798000336, -0.02060101367533207, 102.04458618164062], + [0.09554476290941238, 1.8756707906723022, -0.6875537633895874, -69.5492172241211], + [0.013066126964986324, 0.6877381801605225, 1.877989649772644, -67.09413146972656], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 64f73066e99d823d8749f2403c9d1d61830a1fe3 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:25:08 -0400 Subject: [PATCH 332/463] fix complex event files --- ...g_events.tsv => sub-03_ses-017_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-03_ses-017_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-03_ses-017_task-mario3_run-03_events.tsv} | 0 .../func/sub-03_ses-017_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-03_ses-017_task-mario3_run-04_events.tsv} | 0 .../func/sub-03_ses-017_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-03_ses-017_task-mario3_run-04_part-phase_events.tsv | 1 - ...g_events.tsv => sub-03_ses-017_task-mario3_run-05_events.tsv} | 0 .../func/sub-03_ses-017_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-03_ses-017_task-mario3_run-05_part-phase_events.tsv | 1 - 10 files changed, 5 deletions(-) rename sub-03/ses-017/func/{sub-03_ses-017_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-017_task-mario3_run-01_events.tsv} (100%) rename sub-03/ses-017/func/{sub-03_ses-017_task-mario3_run-01_part-phase_events.tsv => sub-03_ses-017_task-mario3_run-02_events.tsv} (100%) rename sub-03/ses-017/func/{sub-03_ses-017_task-mario3_run-02_part-mag_events.tsv => sub-03_ses-017_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-03_part-phase_events.tsv rename sub-03/ses-017/func/{sub-03_ses-017_task-mario3_run-02_part-phase_events.tsv => sub-03_ses-017_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-04_part-phase_events.tsv rename sub-03/ses-017/func/{sub-03_ses-017_task-mario3_run-03_part-mag_events.tsv => sub-03_ses-017_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-05_part-phase_events.tsv diff --git a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-02_events.tsv similarity index 100% rename from sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-01_part-phase_events.tsv rename to sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-02_events.tsv diff --git a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-02_part-mag_events.tsv b/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-03_events.tsv similarity index 100% rename from sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-02_part-mag_events.tsv rename to sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-03_events.tsv diff --git a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-03_part-phase_events.tsv b/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-02_part-phase_events.tsv b/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-04_events.tsv similarity index 100% rename from sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-02_part-phase_events.tsv rename to sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-04_events.tsv diff --git a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-04_part-mag_events.tsv b/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-04_part-phase_events.tsv b/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-03_part-mag_events.tsv b/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-05_events.tsv similarity index 100% rename from sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-03_part-mag_events.tsv rename to sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-05_events.tsv diff --git a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-05_part-mag_events.tsv b/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-05_part-phase_events.tsv b/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 51a0b558c595e299e62f855c901adab2b22e9f1b Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:25:21 -0400 Subject: [PATCH 333/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..f72a90a4b --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = b8aed7a7-1c9d-40da-9c1d-16f5a40ad65c diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..3a1b9d34c --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 3a1b9d34cfbcfa6eb4b2f2d94c06c79e0f5e2d0f From 21725146dd62aa0d78a4a21f543b9296204ec205 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:25:28 -0400 Subject: [PATCH 334/463] fix fmap phase --- ...6_ses-018_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-018_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-018_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-018_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-018_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-018_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-06/ses-018/sub-06_ses-018_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-06/ses-018/fmap/{sub-06_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-06_ses-018_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-018/fmap/{sub-06_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-018_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-018/fmap/{sub-06_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-06_ses-018_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-018/fmap/{sub-06_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-018_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-018/fmap/{sub-06_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-06_ses-018_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-06/ses-018/fmap/{sub-06_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-06_ses-018_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-06/ses-018/fmap/{sub-06_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-06_ses-018_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-06/ses-018/fmap/{sub-06_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-06_ses-018_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-06/ses-018/fmap/{sub-06_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-06_ses-018_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-06/ses-018/fmap/{sub-06_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-06_ses-018_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 60dd8d1f0..000000000 --- a/sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:59:41.767500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999261, -0.0333538, 0.0191044, 0.0378637, 0.939719, -0.339846], - "ImageOrientationText": "Tra>Cor(-19.9)>Sag(0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0440661, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [589, -7288, -8814, 517, 42, -287, -163, 57], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 241.173, - "WipMemBlock": "15974a45-35dd-4e3d-a3f1-069ed9d0fcfd||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9985220432281494, 0.07572740316390991, 0.013235163874924183, 103.80171966552734], - [0.06670759618282318, 1.8794374465942383, -0.6806355714797974, -68.4758071899414], - [0.03820871561765671, 0.6796911358833313, 1.8805744647979736, -64.08352661132812], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99926100074527, -0.0333537991531, 0.01910435739891, 0.03786370292548, 0.93971874922521, -0.3398455713341], - "ImagePositionPatient": [-866.62842675766, -784.93993777643, 239.4242673561], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.25905, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "155737.296000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.04406606652417, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "160028.167000", - "SliceLocation": -36.266465250793, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000438609, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "155737.223000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["155941.767500", "155943.257500", "155944.747500"], - "ContentTime": ["160028.169000", "160028.172000", "160028.175000"], - "InstanceCreationTime": ["160028.169000", "160028.172000", "160028.175000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4874.0, 4876.0, 4874.0], - "WindowWidth": [18664.0, 18668.0, 18652.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 0b7e9df64..000000000 --- a/sub-06/ses-018/fmap/sub-06_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/6G/Qq/MD5E-s3335798--87e20ad68457f4897fce29880ee4877f.nii.gz/MD5E-s3335798--87e20ad68457f4897fce29880ee4877f.nii.gz \ No newline at end of file diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 59cda21fb..000000000 --- a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:59:31.337500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999261, - -0.0333538, - 0.0191044, - 0.0378637, - 0.939719, - -0.339846 - ], - "ImageOrientationText": "Tra>Cor(-19.9)>Sag(0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0440661, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 589, - -7288, - -8814, - 517, - 42, - -287, - -163, - 57 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 241.173, - "WipMemBlock": "15974a45-35dd-4e3d-a3f1-069ed9d0fcfd||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index b9529e457..000000000 --- a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/X6/3F/MD5E-s1112438--370caa4d6d2742599a0a81683188f587.nii.gz/MD5E-s1112438--370caa4d6d2742599a0a81683188f587.nii.gz \ No newline at end of file diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index d040aaf5b..000000000 --- a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:02:28.137500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": 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"ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.055255, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 589, - -7288, - -8814, - 517, - 42, - -287, - -163, - 57 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 241.173, - "WipMemBlock": "37714b2f-e6c8-4e30-83f5-48765fe66e0e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 3de545b22..000000000 --- a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/zV/V3/MD5E-s1103813--032626d7d5836a9b238fc90f6211634e.nii.gz/MD5E-s1103813--032626d7d5836a9b238fc90f6211634e.nii.gz \ No newline at end of file diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index d9e46a054..000000000 --- a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:15:29.260000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999261, - -0.0333538, - 0.0191044, - 0.0378637, - 0.939719, - -0.339846 - ], - "ImageOrientationText": "Tra>Cor(-19.9)>Sag(0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.055255, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 589, - -7288, - -8814, - 517, - 42, - -287, - -163, - 57 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 241.173, - "WipMemBlock": "dced6a95-5a05-40ee-909c-789cf891813f||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 1b51d278f..000000000 --- a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/2j/MJ/MD5E-s1103821--0a5c10745b1e37493471e947cfbd3c4f.nii.gz/MD5E-s1103821--0a5c10745b1e37493471e947cfbd3c4f.nii.gz \ No newline at end of file diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 66531b6ab..000000000 --- a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:28:54.790000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999261, - -0.0333538, - 0.0191044, - 0.0378637, - 0.939719, - -0.339846 - ], - "ImageOrientationText": "Tra>Cor(-19.9)>Sag(0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.055255, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 589, - -7288, - -8814, - 517, - 42, - -287, - -163, - 57 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 241.173, - "WipMemBlock": "981c642b-80bf-49ef-bd3d-faf02de93db9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 148f95f98..000000000 --- a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/VF/MK/MD5E-s1103765--30071e456e76a088d95ed715202bacd8.nii.gz/MD5E-s1103765--30071e456e76a088d95ed715202bacd8.nii.gz \ No newline at end of file diff --git a/sub-06/ses-018/sub-06_ses-018_scans.tsv b/sub-06/ses-018/sub-06_ses-018_scans.tsv index 39a21f2d8..6bb6f9052 120000 --- a/sub-06/ses-018/sub-06_ses-018_scans.tsv +++ b/sub-06/ses-018/sub-06_ses-018_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/1z/kv/MD5E-s2660--33b5e0496b215e9da0d9e599112605fa.tsv/MD5E-s2660--33b5e0496b215e9da0d9e599112605fa.tsv \ No newline at end of file +../../.git/annex/objects/8p/m9/MD5E-s2059--7b897af701c09ab4a11bbc5e0781db4c.tsv/MD5E-s2059--7b897af701c09ab4a11bbc5e0781db4c.tsv \ No newline at end of file From d749bdaaa40866b213e1d3ba5993d15e1e4d5acd Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:25:43 -0400 Subject: [PATCH 335/463] fix complex event files --- ...g_events.tsv => sub-06_ses-018_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-06_ses-018_task-mario3_run-02_events.tsv} | 0 .../func/sub-06_ses-018_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-06_ses-018_task-mario3_run-03_events.tsv} | 0 .../func/sub-06_ses-018_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-06_ses-018_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-06/ses-018/func/{sub-06_ses-018_task-mario3_run-01_part-mag_events.tsv => sub-06_ses-018_task-mario3_run-01_events.tsv} (100%) rename sub-06/ses-018/func/{sub-06_ses-018_task-mario3_run-01_part-phase_events.tsv => sub-06_ses-018_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-02_part-phase_events.tsv rename sub-06/ses-018/func/{sub-06_ses-018_task-mario3_run-02_part-mag_events.tsv => sub-06_ses-018_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-01_part-mag_events.tsv b/sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-01_events.tsv similarity index 100% rename from sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-01_part-mag_events.tsv rename to sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-01_events.tsv diff --git a/sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-01_part-phase_events.tsv b/sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-02_events.tsv similarity index 100% rename from sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-01_part-phase_events.tsv rename to sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-02_events.tsv diff --git a/sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-02_part-phase_events.tsv b/sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-02_part-mag_events.tsv b/sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_events.tsv similarity index 100% rename from sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-02_part-mag_events.tsv rename to sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_events.tsv diff --git a/sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-mag_events.tsv b/sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-phase_events.tsv b/sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-018/func/sub-06_ses-018_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From e41adb689853ac088273cce35fed40026182a3cc Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:26:09 -0400 Subject: [PATCH 336/463] fix fmap phase --- ...6_ses-012_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-012_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-012_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-012_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-012_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-012_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-012_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-012_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-012_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-012_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-06/ses-012/sub-06_ses-012_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-06/ses-012/fmap/{sub-06_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-06_ses-012_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-012/fmap/{sub-06_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-012_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-012/fmap/sub-06_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-012/fmap/sub-06_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-012/fmap/{sub-06_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-06_ses-012_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-012/fmap/{sub-06_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-012_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-012/fmap/{sub-06_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-06_ses-012_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-06/ses-012/fmap/{sub-06_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-06_ses-012_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-06/ses-012/fmap/{sub-06_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-06_ses-012_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-06/ses-012/fmap/{sub-06_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-06_ses-012_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-06/ses-012/fmap/{sub-06_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-06_ses-012_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-06/ses-012/fmap/{sub-06_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-06_ses-012_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-012/fmap/sub-06_ses-012_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-012/fmap/sub-06_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-012/fmap/sub-06_ses-012_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-012/fmap/sub-06_ses-012_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-012/fmap/sub-06_ses-012_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-012/fmap/sub-06_ses-012_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-012/fmap/sub-06_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 0a7dba6aa..000000000 --- a/sub-06/ses-012/fmap/sub-06_ses-012_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:18:58.475000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.998837, -0.0477724, 0.00653306, 0.0471039, 0.937835, -0.343869], - "ImageOrientationText": "Tra>Cor(-20.1)>Sag(-0.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0329631, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [624, -7262, -8829, 527, 23, -242, -78, -15], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.08, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875, 0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.08, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875, 0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.08, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875, 0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.08, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.674, - "WipMemBlock": "afee6d62-53ea-4f75-9041-126b23e0770c||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.997673749923706, 0.09420786798000336, -0.02060101367533207, 102.04458618164062], - [0.09554476290941238, 1.8756707906723022, -0.6875537633895874, -69.5492172241211], - [0.013066126964986324, 0.6877381801605225, 1.877989649772644, -67.09413146972656], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99883688297538, -0.0477723800124, 0.00653306329246, 0.04710393567054, 0.93783541142682, 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a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 848af5204..000000000 --- a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:18:48.045000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - 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2bee2869e..000000000 --- a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/JK/22/MD5E-s1112367--a9267740278dd9abe98da1977ce40173.nii.gz/MD5E-s1112367--a9267740278dd9abe98da1977ce40173.nii.gz \ No newline at end of file diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 64c0c976b..000000000 --- a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:20:18.325000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - 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"PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0413329, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 624, - -7262, - -8829, - 527, - 23, - -242, - -78, - -15 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 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-../../../.git/annex/objects/G4/Zj/MD5E-s1103589--529b87bd6a1700bb5db0c2572609ef77.nii.gz/MD5E-s1103589--529b87bd6a1700bb5db0c2572609ef77.nii.gz \ No newline at end of file diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 72e7a2775..000000000 --- a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:31:57.532500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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"%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0413329, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 624, - -7262, - -8829, - 527, - 23, - -242, - -78, - -15 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.674, - "WipMemBlock": "db7a710a-c3ca-4774-81b5-0703026c686d||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 40fd22ddd..000000000 --- a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/67/0G/MD5E-s1103604--06c5ebf9f2a1febbfc8fb14d82a38dd2.nii.gz/MD5E-s1103604--06c5ebf9f2a1febbfc8fb14d82a38dd2.nii.gz \ No newline at end of file diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 543513bb7..000000000 --- a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:45:2.252500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998837, - -0.0477724, - 0.00653306, - 0.0471039, - 0.937835, - -0.343869 - ], - "ImageOrientationText": "Tra>Cor(-20.1)>Sag(-0.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0413329, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 624, - -7262, - -8829, - 527, - 23, - -242, - -78, - -15 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 229.674, - "WipMemBlock": "fa6b0374-01e0-4074-a3f2-8ec13743ade9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index e01543e2f..000000000 --- a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Jx/kF/MD5E-s1103729--5479eeb4325cbd4b9da96e268d344fa5.nii.gz/MD5E-s1103729--5479eeb4325cbd4b9da96e268d344fa5.nii.gz \ No newline at end of file diff --git a/sub-06/ses-012/sub-06_ses-012_scans.tsv b/sub-06/ses-012/sub-06_ses-012_scans.tsv index e9012f9a9..75d260706 120000 --- a/sub-06/ses-012/sub-06_ses-012_scans.tsv +++ b/sub-06/ses-012/sub-06_ses-012_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/98/Xx/MD5E-s2667--f5a1d35ec63c70dc9885b1132fa4898b.tsv/MD5E-s2667--f5a1d35ec63c70dc9885b1132fa4898b.tsv \ No newline at end of file +../../.git/annex/objects/9P/X5/MD5E-s2066--2aca7f0028405655d1e013db84aff6b4.tsv/MD5E-s2066--2aca7f0028405655d1e013db84aff6b4.tsv \ No newline at end of file From 9df11df6ecf56e4eee8ccda1398c842e6e5553df Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:26:11 -0400 Subject: [PATCH 337/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-06_ses-009_acq-axial_localizer.json | 81 +++ .../sub-06_ses-009_acq-axial_localizer.nii.gz | 1 + .../sub-06_ses-009_acq-coronal_localizer.json | 81 +++ ...ub-06_ses-009_acq-coronal_localizer.nii.gz | 1 + ...sub-06_ses-009_acq-sagittal_localizer.json | 86 +++ ...b-06_ses-009_acq-sagittal_localizer.nii.gz | 1 + sub-06/ses-009/anat/sub-06_ses-009_scout.json | 542 ++++++++++++++++++ .../ses-009/anat/sub-06_ses-009_scout.nii.gz | 1 + ...9_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-009_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...09_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...009_task-mario3_run-01_part-mag_events.tsv | 1 + ...009_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...09_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-01_part-phase_events.tsv | 1 + ...9_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-009_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...09_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...009_task-mario3_run-02_part-mag_events.tsv | 1 + ...009_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...09_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-02_part-phase_events.tsv | 1 + ...9_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-009_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...09_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...009_task-mario3_run-03_part-mag_events.tsv | 1 + ...009_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...09_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-03_part-phase_events.tsv | 1 + ...9_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-06/ses-009/sub-06_ses-009_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-06/ses-009/anat/sub-06_ses-009_acq-axial_localizer.json create mode 120000 sub-06/ses-009/anat/sub-06_ses-009_acq-axial_localizer.nii.gz create mode 100644 sub-06/ses-009/anat/sub-06_ses-009_acq-coronal_localizer.json create mode 120000 sub-06/ses-009/anat/sub-06_ses-009_acq-coronal_localizer.nii.gz create mode 100644 sub-06/ses-009/anat/sub-06_ses-009_acq-sagittal_localizer.json create mode 120000 sub-06/ses-009/anat/sub-06_ses-009_acq-sagittal_localizer.nii.gz create mode 100644 sub-06/ses-009/anat/sub-06_ses-009_scout.json create mode 120000 sub-06/ses-009/anat/sub-06_ses-009_scout.nii.gz create mode 100644 sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-06/ses-009/sub-06_ses-009_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 3a1b9d34c..cc0ca2c77 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 3a1b9d34cfbcfa6eb4b2f2d94c06c79e0f5e2d0f +Subproject commit cc0ca2c7783ee0c7511cac6e32471ad932b4c879 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..db37a3f34 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-06 41 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-06/ses-009/anat/sub-06_ses-009_acq-axial_localizer.json b/sub-06/ses-009/anat/sub-06_ses-009_acq-axial_localizer.json new file mode 100644 index 000000000..64c9440ac --- /dev/null +++ b/sub-06/ses-009/anat/sub-06_ses-009_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:45:38.035000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + 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1.5675, + 1.6675, + 1.765, + 1.8625, + 1.96, + 2.0575, + 2.1575, + 2.255, + 2.3525, + 2.45, + 2.5475, + 2.6475, + 2.745, + 2.8425, + 2.94, + 3.0375, + 3.1375, + 3.235, + 3.3325, + 3.43, + 3.5275, + 3.6275, + 3.725, + 3.8225, + 3.92, + 4.0175, + 4.1175, + 4.215, + 4.3125, + 4.41, + 4.5075, + 4.6075, + 4.705, + 4.8025, + 4.9, + 4.9975, + 5.0975, + 5.195, + 5.2925, + 5.39, + 5.4875, + 5.5875, + 5.685, + 5.7825 + ], + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 251.2, + "WipMemBlock": "95f0451a-49cb-4ae5-89c3-4d164077f8e9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-phase_sbref.nii.gz b/sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-phase_sbref.nii.gz new file mode 120000 index 000000000..0bea84281 --- /dev/null +++ b/sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/w2/90/MD5E-s1103664--79f8777eb727e9cda6a54a78809e153a.nii.gz/MD5E-s1103664--79f8777eb727e9cda6a54a78809e153a.nii.gz \ No newline at end of file diff --git a/sub-06/ses-009/sub-06_ses-009_scans.tsv b/sub-06/ses-009/sub-06_ses-009_scans.tsv new file mode 120000 index 000000000..6b9841ee8 --- /dev/null +++ b/sub-06/ses-009/sub-06_ses-009_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/Kz/98/MD5E-s2660--f00f4a4625bc31bd51d2ec48fc21b7f1.tsv/MD5E-s2660--f00f4a4625bc31bd51d2ec48fc21b7f1.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..63283e368 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999471, -0.0323902, -0.00290718, 0.0287907, 0.922868, -0.384038], + "ImageOrientationText": "Tra>Cor(-22.6)>Sag(-0.9)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0557735, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [623, -7255, -8819, 518, 2, -203, -114, -3], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 251.2, + "dcmmeta_affine": [ + [-1.9989421367645264, 0.057581305503845215, -0.030244046822190285, 104.54354858398438], + [0.06478041410446167, 1.8457362651824951, -0.7675030827522278, -65.29047393798828], + [-0.005814352072775364, 0.7680767178535461, 1.8466250896453857, -61.71562957763672], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 18e3d905665311503e41eac61f7be98e768804ca Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:26:26 -0400 Subject: [PATCH 338/463] fix complex event files --- ...g_events.tsv => sub-06_ses-012_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-06_ses-012_task-mario3_run-02_events.tsv} | 0 .../func/sub-06_ses-012_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-06_ses-012_task-mario3_run-03_events.tsv} | 0 .../func/sub-06_ses-012_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-06_ses-012_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-06/ses-012/func/{sub-06_ses-012_task-mario3_run-01_part-mag_events.tsv => sub-06_ses-012_task-mario3_run-01_events.tsv} (100%) rename sub-06/ses-012/func/{sub-06_ses-012_task-mario3_run-01_part-phase_events.tsv => sub-06_ses-012_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-02_part-phase_events.tsv rename sub-06/ses-012/func/{sub-06_ses-012_task-mario3_run-02_part-mag_events.tsv => sub-06_ses-012_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-01_part-mag_events.tsv b/sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-01_events.tsv similarity index 100% rename from sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-01_part-mag_events.tsv rename to sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-01_events.tsv diff --git a/sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-01_part-phase_events.tsv b/sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-02_events.tsv similarity index 100% rename from sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-01_part-phase_events.tsv rename to sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-02_events.tsv diff --git a/sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-02_part-phase_events.tsv b/sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-02_part-mag_events.tsv b/sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_events.tsv similarity index 100% rename from sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-02_part-mag_events.tsv rename to sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_events.tsv diff --git a/sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-mag_events.tsv b/sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-phase_events.tsv b/sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-012/func/sub-06_ses-012_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From d699c291926c05348c70b11bfbe6175face02417 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:27:06 -0400 Subject: [PATCH 339/463] fill IntendedFor --- ...3_ses-017_acq-sbref_dir-AP_run-01_epi.json | 92 +++---------------- ...3_ses-017_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...3_ses-017_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...3_ses-017_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...3_ses-017_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- ...3_ses-017_acq-sbref_dir-PA_run-05_epi.json | 88 ++---------------- 6 files changed, 46 insertions(+), 486 deletions(-) diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_epi.json index e4e38b415..7b25c649a 100644 --- a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999979, - 0.00617039, - -0.00191991, - -0.00645766, - 0.965269, - -0.261178 - ], + "ImageOrientationPatientDICOM": [0.999979, 0.00617039, -0.00191991, -0.00645766, 0.965269, -0.261178], "ImageOrientationText": "Tra>Cor(-15.1)>Sag(-0.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,19 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-03_ses-017_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-017/func/sub-03_ses-017_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-017/func/sub-03_ses-017_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-017/func/sub-03_ses-017_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-017/func/sub-03_ses-017_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +67,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 613, - -7226, - -8776, - 686, - 62, - -75, - 64, - -10 - ], + "ShimSetting": [613, -7226, -8776, 686, 62, -75, 64, -10], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_epi.json b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_epi.json index 5be8ec470..1e7601c16 100644 --- a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999979, - 0.00617039, - -0.00191991, - -0.00645766, - 0.965269, - -0.261178 - ], + "ImageOrientationPatientDICOM": [0.999979, 0.00617039, -0.00191991, -0.00645766, 0.965269, -0.261178], "ImageOrientationText": "Tra>Cor(-15.1)>Sag(-0.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-03_ses-017_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 613, - -7226, - -8776, - 686, - 62, - -75, - 64, - -10 - ], + "ShimSetting": [613, -7226, -8776, 686, 62, -75, 64, -10], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_epi.json b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_epi.json index e3ee71e96..a37fcc055 100644 --- a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999979, - 0.00617039, - -0.00191991, - -0.00645766, - 0.965269, - -0.261178 - ], + "ImageOrientationPatientDICOM": [0.999979, 0.00617039, -0.00191991, -0.00645766, 0.965269, -0.261178], "ImageOrientationText": "Tra>Cor(-15.1)>Sag(-0.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-03_ses-017_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 613, - -7226, - -8776, - 686, - 62, - -75, - 64, - -10 - ], + "ShimSetting": [613, -7226, -8776, 686, 62, -75, 64, -10], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-03_epi.json b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-03_epi.json index 8f8a79924..c4cfdbe09 100644 --- a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999979, - 0.00617039, - -0.00191991, - -0.00645766, - 0.965269, - -0.261178 - ], + "ImageOrientationPatientDICOM": [0.999979, 0.00617039, -0.00191991, -0.00645766, 0.965269, -0.261178], "ImageOrientationText": "Tra>Cor(-15.1)>Sag(-0.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-03_ses-017_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 613, - -7226, - -8776, - 686, - 62, - -75, - 64, - -10 - ], + "ShimSetting": [613, -7226, -8776, 686, 62, -75, 64, -10], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-04_epi.json b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-04_epi.json index aa59e8e82..ed30b00e0 100644 --- a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999979, - 0.00617039, - -0.00191991, - -0.00645766, - 0.965269, - -0.261178 - ], + "ImageOrientationPatientDICOM": [0.999979, 0.00617039, -0.00191991, -0.00645766, 0.965269, -0.261178], "ImageOrientationText": "Tra>Cor(-15.1)>Sag(-0.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-03_ses-017_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 613, - -7226, - -8776, - 686, - 62, - -75, - 64, - -10 - ], + "ShimSetting": [613, -7226, -8776, 686, 62, -75, 64, -10], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_epi.json b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_epi.json index 9dcdcd8e1..208f4fd29 100644 --- a/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-03/ses-017/fmap/sub-03_ses-017_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999979, - 0.00617039, - -0.00191991, - -0.00645766, - 0.965269, - -0.261178 - ], + "ImageOrientationPatientDICOM": [0.999979, 0.00617039, -0.00191991, -0.00645766, 0.965269, -0.261178], "ImageOrientationText": "Tra>Cor(-15.1)>Sag(-0.0)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-03_ses-017_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 613, - -7226, - -8776, - 686, - 62, - -75, - 64, - -10 - ], + "ShimSetting": [613, -7226, -8776, 686, 62, -75, 64, -10], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 7529a0dcfdd97d2a467701bc0d7b5e3a16b55b82 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:27:11 -0400 Subject: [PATCH 340/463] fill IntendedFor --- ...6_ses-018_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...6_ses-018_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...6_ses-018_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...6_ses-018_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_epi.json b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_epi.json index 815148c94..a7ab36d36 100644 --- a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999261, - -0.0333538, - 0.0191044, - 0.0378637, - 0.939719, - -0.339846 - ], + "ImageOrientationPatientDICOM": [0.999261, -0.0333538, 0.0191044, 0.0378637, 0.939719, -0.339846], "ImageOrientationText": "Tra>Cor(-19.9)>Sag(0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-06_ses-018_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-018/func/sub-06_ses-018_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-018/func/sub-06_ses-018_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 589, - -7288, - -8814, - 517, - 42, - -287, - -163, - 57 - ], + "ShimSetting": [589, -7288, -8814, 517, 42, -287, -163, 57], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_epi.json b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_epi.json index 22950071a..0b8bc64bd 100644 --- a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999261, - -0.0333538, - 0.0191044, - 0.0378637, - 0.939719, - -0.339846 - ], + "ImageOrientationPatientDICOM": [0.999261, -0.0333538, 0.0191044, 0.0378637, 0.939719, -0.339846], "ImageOrientationText": "Tra>Cor(-19.9)>Sag(0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-06_ses-018_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 589, - -7288, - -8814, - 517, - 42, - -287, - -163, - 57 - ], + "ShimSetting": [589, -7288, -8814, 517, 42, -287, -163, 57], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_epi.json b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_epi.json index fff5f0a23..1baea07f6 100644 --- a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999261, - -0.0333538, - 0.0191044, - 0.0378637, - 0.939719, - -0.339846 - ], + "ImageOrientationPatientDICOM": [0.999261, -0.0333538, 0.0191044, 0.0378637, 0.939719, -0.339846], "ImageOrientationText": "Tra>Cor(-19.9)>Sag(0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-06_ses-018_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 589, - -7288, - -8814, - 517, - 42, - -287, - -163, - 57 - ], + "ShimSetting": [589, -7288, -8814, 517, 42, -287, -163, 57], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_epi.json b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_epi.json index 781355bb0..1e365b71b 100644 --- a/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-06/ses-018/fmap/sub-06_ses-018_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999261, - -0.0333538, - 0.0191044, - 0.0378637, - 0.939719, - -0.339846 - ], + "ImageOrientationPatientDICOM": [0.999261, -0.0333538, 0.0191044, 0.0378637, 0.939719, -0.339846], "ImageOrientationText": "Tra>Cor(-19.9)>Sag(0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-06_ses-018_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 589, - -7288, - -8814, - 517, - 42, - -287, - -163, - 57 - ], + "ShimSetting": [589, -7288, -8814, 517, 42, -287, -163, 57], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From de71763b4a85a31da408d4021d0941c4d6a6e592 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:27:16 -0400 Subject: [PATCH 341/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-03_ses-018_acq-axial_localizer.json | 81 +++ .../sub-03_ses-018_acq-axial_localizer.nii.gz | 1 + .../sub-03_ses-018_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-018_acq-coronal_localizer.nii.gz | 1 + ...sub-03_ses-018_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-018_acq-sagittal_localizer.nii.gz | 1 + sub-03/ses-018/anat/sub-03_ses-018_scout.json | 542 ++++++++++++++++++ .../ses-018/anat/sub-03_ses-018_scout.nii.gz | 1 + ...8_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-06_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-06_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 + ...-018_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...18_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...018_task-mario3_run-01_part-mag_events.tsv | 1 + ...018_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...18_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-01_part-phase_events.tsv | 1 + ...8_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-018_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...18_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...018_task-mario3_run-02_part-mag_events.tsv | 1 + ...018_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...18_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-02_part-phase_events.tsv | 1 + ...8_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-018_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...18_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...018_task-mario3_run-03_part-mag_events.tsv | 1 + ...018_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...18_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-03_part-phase_events.tsv | 1 + ...8_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-018_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...18_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...018_task-mario3_run-04_part-mag_events.tsv | 1 + ...018_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...18_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-04_part-phase_events.tsv | 1 + ...8_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-018_task-mario3_run-05_part-mag_bold.json | 172 ++++++ ...18_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...018_task-mario3_run-05_part-mag_events.tsv | 1 + ...018_task-mario3_run-05_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...18_task-mario3_run-05_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-05_part-phase_events.tsv | 1 + ...8_task-mario3_run-05_part-phase_sbref.json | 153 +++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + ...-018_task-mario3_run-06_part-mag_bold.json | 172 ++++++ ...18_task-mario3_run-06_part-mag_bold.nii.gz | 1 + ...018_task-mario3_run-06_part-mag_events.tsv | 1 + ...018_task-mario3_run-06_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-06_part-mag_sbref.nii.gz | 1 + ...18_task-mario3_run-06_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-06_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-06_part-phase_events.tsv | 1 + ...8_task-mario3_run-06_part-phase_sbref.json | 153 +++++ ...task-mario3_run-06_part-phase_sbref.nii.gz | 1 + sub-03/ses-018/sub-03_ses-018_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 107 files changed, 7333 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-018/anat/sub-03_ses-018_acq-axial_localizer.json create mode 120000 sub-03/ses-018/anat/sub-03_ses-018_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-018/anat/sub-03_ses-018_acq-coronal_localizer.json create mode 120000 sub-03/ses-018/anat/sub-03_ses-018_acq-coronal_localizer.nii.gz create mode 100644 sub-03/ses-018/anat/sub-03_ses-018_acq-sagittal_localizer.json create mode 120000 sub-03/ses-018/anat/sub-03_ses-018_acq-sagittal_localizer.nii.gz create mode 100644 sub-03/ses-018/anat/sub-03_ses-018_scout.json create mode 120000 sub-03/ses-018/anat/sub-03_ses-018_scout.nii.gz create mode 100644 sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 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sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-06_part-phase_sbref.nii.gz create mode 120000 sub-03/ses-018/sub-03_ses-018_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index f189624ce..0708174ed 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit f189624ce791255adaab9b3e272d090b3f90620e +Subproject commit 0708174eda5fa29ed05deec4c8e9f9bcdf6f369e diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-03/ses-018/anat/sub-03_ses-018_acq-axial_localizer.json b/sub-03/ses-018/anat/sub-03_ses-018_acq-axial_localizer.json new file mode 100644 index 000000000..041c14c34 --- /dev/null +++ b/sub-03/ses-018/anat/sub-03_ses-018_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "13:23:37.015000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + 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file diff --git a/sub-03/ses-018/anat/sub-03_ses-018_acq-coronal_localizer.json b/sub-03/ses-018/anat/sub-03_ses-018_acq-coronal_localizer.json new file mode 100644 index 000000000..3f918232c --- /dev/null +++ b/sub-03/ses-018/anat/sub-03_ses-018_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "13:23:44.005000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + 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b/sub-03/ses-018/anat/sub-03_ses-018_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "13:23:30.025000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 0, + 1, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Sag", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, 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b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-06_part-phase_events.tsv @@ -0,0 +1 @@ +../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-06_part-phase_sbref.json b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-06_part-phase_sbref.json new file mode 100644 index 000000000..8fe5b5dd1 --- /dev/null +++ b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-06_part-phase_sbref.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "14:21:27.665000", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 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"http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999258, 0.0303676, 0.0236755, -0.0228508, 0.962543, -0.270165], + "ImageOrientationText": "Tra>Cor(-15.6)>Sag(1.8)", + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0458441, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [627, -7201, -8753, 691, 75, 50, 40, -19], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 212.617, + "dcmmeta_affine": [ + [-1.9985166788101196, -0.04570164903998375, 0.061985865235328674, 109.50057220458984], + [-0.06073527783155441, 1.9250859022140503, -0.5388465523719788, -69.95941162109375], + [0.04735096916556358, 0.5403293371200562, 1.9250459671020508, -55.88344955444336], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 9feabb57f728c163be69b34eb81cc20b87e6df3b Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:27:35 -0400 Subject: [PATCH 342/463] fix fmap phase --- ...6_ses-009_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-009_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-009_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-009_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-009_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-009_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-06/ses-009/sub-06_ses-009_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-06/ses-009/fmap/{sub-06_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-06_ses-009_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-009/fmap/{sub-06_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-009_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-009/fmap/{sub-06_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-06_ses-009_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-009/fmap/{sub-06_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-009_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-009/fmap/{sub-06_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-06_ses-009_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-06/ses-009/fmap/{sub-06_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-06_ses-009_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-06/ses-009/fmap/{sub-06_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-06_ses-009_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-06/ses-009/fmap/{sub-06_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-06_ses-009_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-06/ses-009/fmap/{sub-06_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-06_ses-009_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-06/ses-009/fmap/{sub-06_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-06_ses-009_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index b1bfbf254..000000000 --- a/sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:46:43.970000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 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0.39, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685, 0, 0.7825, 0.0975, 0.88, 0.195, 0.9775, 0.2925, 1.0775, 0.39, 1.175, 0.49, 1.2725, 0.5875, 1.37, 0.685], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.2, - "WipMemBlock": "ab18e988-d7fd-4077-8662-adfce4dcdec7||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9989421367645264, 0.057581305503845215, -0.030244046822190285, 104.54354858398438], - [0.06478041410446167, 1.8457362651824951, -0.7675030827522278, -65.29047393798828], - [-0.005814352072775364, 0.7680767178535461, 1.8466250896453857, -61.71562957763672], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - 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"PerformedProcedureStepStartTime": "154450.897000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.04447959922543, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "154729.764000", - "SliceLocation": -33.508406906232, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000237687, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "154450.805000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenter": 4802.0, - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["154643.970000", "154645.460000", "154646.950000"], - "ContentTime": ["154729.766000", "154729.769000", "154729.771000"], - "InstanceCreationTime": ["154729.766000", "154729.769000", "154729.771000"], - "InstanceNumber": [1, 2, 3], - "WindowWidth": [18616.0, 18618.0, 18612.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 369cadcea..000000000 --- a/sub-06/ses-009/fmap/sub-06_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/qX/42/MD5E-s3334727--049e6899d1ec3ebd89e05f7dcd1f294f.nii.gz/MD5E-s3334727--049e6899d1ec3ebd89e05f7dcd1f294f.nii.gz \ No newline at end of file diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index b9f8f1174..000000000 --- a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:46:33.540000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999471, - -0.0323902, - -0.00290718, - 0.0287907, - 0.922868, - -0.384038 - ], - "ImageOrientationText": "Tra>Cor(-22.6)>Sag(-0.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0444796, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 623, - -7255, - -8819, - 518, - 2, - -203, - -114, - -3 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.2, - "WipMemBlock": "ab18e988-d7fd-4077-8662-adfce4dcdec7||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 2112c6dc4..000000000 --- a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/76/5v/MD5E-s1112490--bb7ae79454df4fd07202ab8d8a641d71.nii.gz/MD5E-s1112490--bb7ae79454df4fd07202ab8d8a641d71.nii.gz \ No newline at end of file diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index b0915b7fd..000000000 --- a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:47:56.587500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999471, - -0.0323902, - -0.00290718, - 0.0287907, - 0.922868, - -0.384038 - ], - "ImageOrientationText": "Tra>Cor(-22.6)>Sag(-0.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0557735, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 623, - -7255, - -8819, - 518, - 2, - -203, - -114, - -3 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.2, - "WipMemBlock": "1fc51bd6-250b-4322-a178-eb244b6ecda0||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 5e4150422..000000000 --- a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/kp/vg/MD5E-s1103440--da35a3b5aba53b0339453916dd516ebe.nii.gz/MD5E-s1103440--da35a3b5aba53b0339453916dd516ebe.nii.gz \ No newline at end of file diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 9e2a608b5..000000000 --- a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:00:15.400000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999471, - -0.0323902, - -0.00290718, - 0.0287907, - 0.922868, - -0.384038 - ], - "ImageOrientationText": "Tra>Cor(-22.6)>Sag(-0.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0557735, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 623, - -7255, - -8819, - 518, - 2, - -203, - -114, - -3 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.2, - "WipMemBlock": "c3d73607-bc70-4b24-9ec2-898b3548cc43||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index f5f1a4629..000000000 --- a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/26/xZ/MD5E-s1103695--2c6ab6739a98bfa04751e4454f1541ce.nii.gz/MD5E-s1103695--2c6ab6739a98bfa04751e4454f1541ce.nii.gz \ No newline at end of file diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 691ee4932..000000000 --- a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:09:37.007500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999471, - -0.0323902, - -0.00290718, - 0.0287907, - 0.922868, - -0.384038 - ], - "ImageOrientationText": "Tra>Cor(-22.6)>Sag(-0.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0557735, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 623, - -7255, - -8819, - 518, - 2, - -203, - -114, - -3 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.2, - "WipMemBlock": "95f0451a-49cb-4ae5-89c3-4d164077f8e9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 0bea84281..000000000 --- a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/w2/90/MD5E-s1103664--79f8777eb727e9cda6a54a78809e153a.nii.gz/MD5E-s1103664--79f8777eb727e9cda6a54a78809e153a.nii.gz \ No newline at end of file diff --git a/sub-06/ses-009/sub-06_ses-009_scans.tsv b/sub-06/ses-009/sub-06_ses-009_scans.tsv index 6b9841ee8..f33827a8f 120000 --- a/sub-06/ses-009/sub-06_ses-009_scans.tsv +++ b/sub-06/ses-009/sub-06_ses-009_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/Kz/98/MD5E-s2660--f00f4a4625bc31bd51d2ec48fc21b7f1.tsv/MD5E-s2660--f00f4a4625bc31bd51d2ec48fc21b7f1.tsv \ No newline at end of file +../../.git/annex/objects/22/6k/MD5E-s2059--e11e14531a098591568b22f2c4f95874.tsv/MD5E-s2059--e11e14531a098591568b22f2c4f95874.tsv \ No newline at end of file From 46268db228950692012866a750a2c1660b4892df Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:27:41 -0400 Subject: [PATCH 343/463] fill IntendedFor --- ...6_ses-012_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...6_ses-012_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...6_ses-012_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...6_ses-012_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-AP_run-01_epi.json b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-AP_run-01_epi.json index 48bd1fe25..b3b14f233 100644 --- a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998837, - -0.0477724, - 0.00653306, - 0.0471039, - 0.937835, - -0.343869 - ], + "ImageOrientationPatientDICOM": [0.998837, -0.0477724, 0.00653306, 0.0471039, 0.937835, -0.343869], "ImageOrientationText": "Tra>Cor(-20.1)>Sag(-0.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-012/func/sub-06_ses-012_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-012/func/sub-06_ses-012_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-012/func/sub-06_ses-012_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 624, - -7262, - -8829, - 527, - 23, - -242, - -78, - -15 - ], + "ShimSetting": [624, -7262, -8829, 527, 23, -242, -78, -15], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.02, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_epi.json b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_epi.json index 63964b966..5cb6be282 100644 --- a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998837, - -0.0477724, - 0.00653306, - 0.0471039, - 0.937835, - -0.343869 - ], + "ImageOrientationPatientDICOM": [0.998837, -0.0477724, 0.00653306, 0.0471039, 0.937835, -0.343869], "ImageOrientationText": "Tra>Cor(-20.1)>Sag(-0.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-012/func/sub-06_ses-012_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 624, - -7262, - -8829, - 527, - 23, - -242, - -78, - -15 - ], + "ShimSetting": [624, -7262, -8829, 527, 23, -242, -78, -15], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_epi.json b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_epi.json index 3fbce4806..25ca53b37 100644 --- a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998837, - -0.0477724, - 0.00653306, - 0.0471039, - 0.937835, - -0.343869 - ], + "ImageOrientationPatientDICOM": [0.998837, -0.0477724, 0.00653306, 0.0471039, 0.937835, -0.343869], "ImageOrientationText": "Tra>Cor(-20.1)>Sag(-0.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-012/func/sub-06_ses-012_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 624, - -7262, - -8829, - 527, - 23, - -242, - -78, - -15 - ], + "ShimSetting": [624, -7262, -8829, 527, 23, -242, -78, -15], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_epi.json b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_epi.json index b4588f358..3b2c78d56 100644 --- a/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-06/ses-012/fmap/sub-06_ses-012_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998837, - -0.0477724, - 0.00653306, - 0.0471039, - 0.937835, - -0.343869 - ], + "ImageOrientationPatientDICOM": [0.998837, -0.0477724, 0.00653306, 0.0471039, 0.937835, -0.343869], "ImageOrientationText": "Tra>Cor(-20.1)>Sag(-0.6)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-012/func/sub-06_ses-012_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 624, - -7262, - -8829, - 527, - 23, - -242, - -78, - -15 - ], + "ShimSetting": [624, -7262, -8829, 527, 23, -242, -78, -15], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From d0ab9ac9cd1e41625c8a1f145f792347e7e42fd9 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:28:04 -0400 Subject: [PATCH 344/463] fix complex event files --- ...g_events.tsv => sub-06_ses-009_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-06_ses-009_task-mario3_run-02_events.tsv} | 0 .../func/sub-06_ses-009_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-06_ses-009_task-mario3_run-03_events.tsv} | 0 .../func/sub-06_ses-009_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-06_ses-009_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-06/ses-009/func/{sub-06_ses-009_task-mario3_run-01_part-mag_events.tsv => sub-06_ses-009_task-mario3_run-01_events.tsv} (100%) rename sub-06/ses-009/func/{sub-06_ses-009_task-mario3_run-01_part-phase_events.tsv => sub-06_ses-009_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-02_part-phase_events.tsv rename sub-06/ses-009/func/{sub-06_ses-009_task-mario3_run-02_part-mag_events.tsv => sub-06_ses-009_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-01_part-mag_events.tsv b/sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-01_events.tsv similarity index 100% rename from sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-01_part-mag_events.tsv rename to sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-01_events.tsv diff --git a/sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-01_part-phase_events.tsv b/sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-02_events.tsv similarity index 100% rename from sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-01_part-phase_events.tsv rename to sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-02_events.tsv diff --git a/sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-02_part-phase_events.tsv b/sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-02_part-mag_events.tsv b/sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_events.tsv similarity index 100% rename from sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-02_part-mag_events.tsv rename to sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_events.tsv diff --git a/sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-mag_events.tsv b/sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-phase_events.tsv b/sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-009/func/sub-06_ses-009_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 9cd9d21acabb21151d0459fd2d52852113f4d917 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:29:14 -0400 Subject: [PATCH 345/463] fill IntendedFor --- ...6_ses-009_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...6_ses-009_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...6_ses-009_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...6_ses-009_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_epi.json b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_epi.json index a8467c338..04b1f1545 100644 --- a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999471, - -0.0323902, - -0.00290718, - 0.0287907, - 0.922868, - -0.384038 - ], + "ImageOrientationPatientDICOM": [0.999471, -0.0323902, -0.00290718, 0.0287907, 0.922868, -0.384038], "ImageOrientationText": "Tra>Cor(-22.6)>Sag(-0.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-009/func/sub-06_ses-009_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-009/func/sub-06_ses-009_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-009/func/sub-06_ses-009_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 623, - -7255, - -8819, - 518, - 2, - -203, - -114, - -3 - ], + "ShimSetting": [623, -7255, -8819, 518, 2, -203, -114, -3], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.9775, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_epi.json b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_epi.json index 18982b736..e7cfbdb85 100644 --- a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999471, - -0.0323902, - -0.00290718, - 0.0287907, - 0.922868, - -0.384038 - ], + "ImageOrientationPatientDICOM": [0.999471, -0.0323902, -0.00290718, 0.0287907, 0.922868, -0.384038], "ImageOrientationText": "Tra>Cor(-22.6)>Sag(-0.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-009/func/sub-06_ses-009_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 623, - -7255, - -8819, - 518, - 2, - -203, - -114, - -3 - ], + "ShimSetting": [623, -7255, -8819, 518, 2, -203, -114, -3], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_epi.json b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_epi.json index 927d1d1ce..ea703837a 100644 --- a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999471, - -0.0323902, - -0.00290718, - 0.0287907, - 0.922868, - -0.384038 - ], + "ImageOrientationPatientDICOM": [0.999471, -0.0323902, -0.00290718, 0.0287907, 0.922868, -0.384038], "ImageOrientationText": "Tra>Cor(-22.6)>Sag(-0.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-009/func/sub-06_ses-009_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 623, - -7255, - -8819, - 518, - 2, - -203, - -114, - -3 - ], + "ShimSetting": [623, -7255, -8819, 518, 2, -203, -114, -3], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_epi.json b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_epi.json index 34217ad41..a7d5f3d2f 100644 --- a/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-06/ses-009/fmap/sub-06_ses-009_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999471, - -0.0323902, - -0.00290718, - 0.0287907, - 0.922868, - -0.384038 - ], + "ImageOrientationPatientDICOM": [0.999471, -0.0323902, -0.00290718, 0.0287907, 0.922868, -0.384038], "ImageOrientationText": "Tra>Cor(-22.6)>Sag(-0.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-009/func/sub-06_ses-009_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 623, - -7255, - -8819, - 518, - 2, - -203, - -114, - -3 - ], + "ShimSetting": [623, -7255, -8819, 518, 2, -203, -114, -3], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 7f2c856126a3155fdc735b5a5d06dcb8fad250cf Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:29:33 -0400 Subject: [PATCH 346/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..4b70b78cc --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = cf0c82d7-d44d-45e1-afe7-efc8638fcdc7 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..f128bb082 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit f128bb082cb9d920dbfe7aeacde4a2acb3b7a9d1 From a2f5ff717489f3113a81c91432e970a0250903bd Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:30:04 -0400 Subject: [PATCH 347/463] fix fmap phase --- ...3_ses-018_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-018_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-018_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-018_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-018_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-018_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-018_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-018_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-PA_run-06_epi.json} | 0 ...es-018_acq-sbref_dir-PA_run-06_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 - sub-03/ses-018/sub-03_ses-018_scans.tsv | 2 +- 33 files changed, 1 insertion(+), 1250 deletions(-) rename sub-03/ses-018/fmap/{sub-03_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-018_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-018/fmap/{sub-03_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-018_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-018/fmap/{sub-03_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-018_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-018/fmap/{sub-03_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-018_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-018/fmap/{sub-03_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-018_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-018/fmap/{sub-03_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-018_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-018/fmap/{sub-03_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-018_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-018/fmap/{sub-03_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-018_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-03/ses-018/fmap/{sub-03_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-03_ses-018_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-03/ses-018/fmap/{sub-03_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-03_ses-018_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-03/ses-018/fmap/{sub-03_ses-018_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-03_ses-018_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-03/ses-018/fmap/{sub-03_ses-018_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-03_ses-018_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-03/ses-018/fmap/{sub-03_ses-018_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-03_ses-018_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-03/ses-018/fmap/{sub-03_ses-018_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-03_ses-018_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz rename sub-03/ses-018/fmap/{sub-03_ses-018_acq-sbref_dir-PA_run-06_part-mag_epi.json => sub-03_ses-018_acq-sbref_dir-PA_run-06_epi.json} (100%) rename sub-03/ses-018/fmap/{sub-03_ses-018_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz => sub-03_ses-018_acq-sbref_dir-PA_run-06_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_part-phase_epi.json delete mode 120000 sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 3f8c18045..000000000 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:30:36.692500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999258, 0.0303676, 0.0236755, -0.0228508, 0.962543, -0.270165], - "ImageOrientationText": "Tra>Cor(-15.6)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - 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"dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99925836395945, 0.030367639462, 0.02367548374564, -0.0228508248174, 0.96254293311826, -0.2701646566619], - "ImagePositionPatient": [-815.61798814501, -851.16333153997, 179.21458718801], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.260395, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "115807.186000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.03656082541134, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "133123.159000", - "SliceLocation": -31.546668105929, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000145847, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "115807.019000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["133036.692500", "133038.182500", "133039.672500"], - "ContentTime": ["133123.161000", "133123.164000", "133123.166000"], - "InstanceCreationTime": ["133123.161000", "133123.164000", "133123.166000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4796.0, 4798.0, 4800.0], - "WindowWidth": [18612.0, 18614.0, 18618.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 6ec737109..000000000 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Jg/QX/MD5E-s3334892--bd5b3f552040cb6a52f533e0c441b4b9.nii.gz/MD5E-s3334892--bd5b3f552040cb6a52f533e0c441b4b9.nii.gz \ No newline at end of file diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index c97f4f66e..000000000 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:30:26.262500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999258, - 0.0303676, - 0.0236755, - -0.0228508, - 0.962543, - -0.270165 - ], - "ImageOrientationText": "Tra>Cor(-15.6)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0365608, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 627, - -7201, - -8753, - 691, - 75, - 50, - 40, - -19 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.51, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 212.617, - "WipMemBlock": "bb83a981-1915-4042-9e29-45ab61632354||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 657145568..000000000 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/vV/mZ/MD5E-s1112402--df5b0ad624a7c75e4eeef7a39b7bc2eb.nii.gz/MD5E-s1112402--df5b0ad624a7c75e4eeef7a39b7bc2eb.nii.gz \ No newline at end of file diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 30cd7777c..000000000 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:32:3.252500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999258, - 0.0303676, - 0.0236755, - -0.0228508, - 0.962543, - -0.270165 - ], - "ImageOrientationText": "Tra>Cor(-15.6)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0458441, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 627, - -7201, - -8753, - 691, - 75, - 50, - 40, - -19 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 212.617, - "WipMemBlock": "f13d888d-3271-45e3-88c3-968250f85ca6||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 41c37205d..000000000 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/7v/PW/MD5E-s1103465--ce62faccc36b47f435e1b95411342824.nii.gz/MD5E-s1103465--ce62faccc36b47f435e1b95411342824.nii.gz \ No newline at end of file diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 4fe967288..000000000 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:41:58.050000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999258, - 0.0303676, - 0.0236755, - -0.0228508, - 0.962543, - -0.270165 - ], - "ImageOrientationText": "Tra>Cor(-15.6)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0458441, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 627, - -7201, - -8753, - 691, - 75, - 50, - 40, - -19 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 212.617, - "WipMemBlock": "3f42eaca-717a-428f-ae06-fe562ea1b7a9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index bf893b05b..000000000 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/j6/4m/MD5E-s1103681--949ec2700dcd24d9b57ca6f016489d20.nii.gz/MD5E-s1103681--949ec2700dcd24d9b57ca6f016489d20.nii.gz \ No newline at end of file diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 2c23c7dbc..000000000 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:51:59.270000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999258, - 0.0303676, - 0.0236755, - -0.0228508, - 0.962543, - -0.270165 - ], - "ImageOrientationText": "Tra>Cor(-15.6)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0458441, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 627, - -7201, - -8753, - 691, - 75, - 50, - 40, - -19 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 212.617, - "WipMemBlock": "ca6f6597-41bb-4406-9bde-133ab6557da6||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index e3ccc2c1f..000000000 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/W9/pZ/MD5E-s1103727--ec58dedda2fb7c19930152df278c7125.nii.gz/MD5E-s1103727--ec58dedda2fb7c19930152df278c7125.nii.gz \ No newline at end of file diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index ee235ccc5..000000000 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:01:27.170000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999258, - 0.0303676, - 0.0236755, - -0.0228508, - 0.962543, - -0.270165 - ], - "ImageOrientationText": "Tra>Cor(-15.6)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0458441, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 627, - -7201, - -8753, - 691, - 75, - 50, - 40, - -19 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 212.617, - "WipMemBlock": "3174ff05-e95d-49e2-a3c7-8f32b16ebe08||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index f0e9e7cea..000000000 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/fz/X6/MD5E-s1103779--0626c653739fb8d985a819ed4c7c7b08.nii.gz/MD5E-s1103779--0626c653739fb8d985a819ed4c7c7b08.nii.gz \ No newline at end of file diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index d6a5b061a..000000000 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:11:47.037500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999258, - 0.0303676, - 0.0236755, - -0.0228508, - 0.962543, - -0.270165 - ], - "ImageOrientationText": "Tra>Cor(-15.6)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-05", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0458441, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 627, - -7201, - -8753, - 691, - 75, - 50, - 40, - -19 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 212.617, - "WipMemBlock": "960348bf-9a1b-4384-987b-92c9a91076af||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index 22ee28e24..000000000 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/j3/M0/MD5E-s1103863--73aa518f8ec365c400a4f4e6a240b7c5.nii.gz/MD5E-s1103863--73aa518f8ec365c400a4f4e6a240b7c5.nii.gz \ No newline at end of file diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_part-mag_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_epi.json similarity index 100% rename from sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_part-mag_epi.json rename to sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_epi.json diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_epi.nii.gz similarity index 100% rename from sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz rename to sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_epi.nii.gz diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_part-phase_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_part-phase_epi.json deleted file mode 100644 index 0d60cf141..000000000 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:21:27.665000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999258, - 0.0303676, - 0.0236755, - -0.0228508, - 0.962543, - -0.270165 - ], - "ImageOrientationText": "Tra>Cor(-15.6)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-06", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0458441, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-06_SBRef", - "SeriesNumber": 24, - "ShimSetting": [ - 627, - -7201, - -8753, - 691, - 75, - 50, - 40, - -19 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 212.617, - "WipMemBlock": "40d17c6d-1f04-490d-8503-fd06bb6e3ae6||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz deleted file mode 120000 index f39c213ea..000000000 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/J6/Fk/MD5E-s1103960--642d40034c63c20133a73a95724361d4.nii.gz/MD5E-s1103960--642d40034c63c20133a73a95724361d4.nii.gz \ No newline at end of file diff --git a/sub-03/ses-018/sub-03_ses-018_scans.tsv b/sub-03/ses-018/sub-03_ses-018_scans.tsv index 168aea05c..2039465c6 120000 --- a/sub-03/ses-018/sub-03_ses-018_scans.tsv +++ b/sub-03/ses-018/sub-03_ses-018_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/1z/8g/MD5E-s4533--0ec345dc53741d9c2810c2a371c4622f.tsv/MD5E-s4533--0ec345dc53741d9c2810c2a371c4622f.tsv \ No newline at end of file +../../.git/annex/objects/4v/PQ/MD5E-s3569--5d46fd46230045b9484a9577c364abe5.tsv/MD5E-s3569--5d46fd46230045b9484a9577c364abe5.tsv \ No newline at end of file From ffab87d5f45aadbd7a4101379c0e67ee34f5d1b3 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:30:22 -0400 Subject: [PATCH 348/463] fix complex event files --- ...g_events.tsv => sub-03_ses-018_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-03_ses-018_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-03_ses-018_task-mario3_run-03_events.tsv} | 0 ...e_events.tsv => sub-03_ses-018_task-mario3_run-04_events.tsv} | 0 .../func/sub-03_ses-018_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-03_ses-018_task-mario3_run-04_part-phase_events.tsv | 1 - ...g_events.tsv => sub-03_ses-018_task-mario3_run-05_events.tsv} | 0 .../func/sub-03_ses-018_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-03_ses-018_task-mario3_run-05_part-phase_events.tsv | 1 - ...e_events.tsv => sub-03_ses-018_task-mario3_run-06_events.tsv} | 0 .../func/sub-03_ses-018_task-mario3_run-06_part-mag_events.tsv | 1 - .../func/sub-03_ses-018_task-mario3_run-06_part-phase_events.tsv | 1 - 12 files changed, 6 deletions(-) rename sub-03/ses-018/func/{sub-03_ses-018_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-018_task-mario3_run-01_events.tsv} (100%) rename sub-03/ses-018/func/{sub-03_ses-018_task-mario3_run-01_part-phase_events.tsv => sub-03_ses-018_task-mario3_run-02_events.tsv} (100%) rename sub-03/ses-018/func/{sub-03_ses-018_task-mario3_run-02_part-mag_events.tsv => sub-03_ses-018_task-mario3_run-03_events.tsv} (100%) rename sub-03/ses-018/func/{sub-03_ses-018_task-mario3_run-02_part-phase_events.tsv => sub-03_ses-018_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-04_part-phase_events.tsv rename sub-03/ses-018/func/{sub-03_ses-018_task-mario3_run-03_part-mag_events.tsv => sub-03_ses-018_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-05_part-phase_events.tsv rename sub-03/ses-018/func/{sub-03_ses-018_task-mario3_run-03_part-phase_events.tsv => sub-03_ses-018_task-mario3_run-06_events.tsv} (100%) delete mode 120000 sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-06_part-mag_events.tsv delete mode 120000 sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-06_part-phase_events.tsv diff --git a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-02_events.tsv similarity index 100% rename from sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-01_part-phase_events.tsv rename to sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-02_events.tsv diff --git a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-02_part-mag_events.tsv b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-03_events.tsv similarity index 100% rename from sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-02_part-mag_events.tsv rename to sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-03_events.tsv diff --git a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-02_part-phase_events.tsv b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-04_events.tsv similarity index 100% rename from sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-02_part-phase_events.tsv rename to sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-04_events.tsv diff --git a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-04_part-mag_events.tsv b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-04_part-phase_events.tsv b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-03_part-mag_events.tsv b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-05_events.tsv similarity index 100% rename from sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-03_part-mag_events.tsv rename to sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-05_events.tsv diff --git a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-05_part-mag_events.tsv b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-05_part-phase_events.tsv b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-03_part-phase_events.tsv b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-06_events.tsv similarity index 100% rename from sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-03_part-phase_events.tsv rename to sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-06_events.tsv diff --git a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-06_part-mag_events.tsv b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-06_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-06_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-06_part-phase_events.tsv b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-06_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-06_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From ec48ec156dbd59a0c8b9cf3ab19f9dafc67d3158 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:30:41 -0400 Subject: [PATCH 349/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-03_ses-015_acq-axial_localizer.json | 81 +++ .../sub-03_ses-015_acq-axial_localizer.nii.gz | 1 + .../sub-03_ses-015_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-015_acq-coronal_localizer.nii.gz | 1 + ...sub-03_ses-015_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-015_acq-sagittal_localizer.nii.gz | 1 + sub-03/ses-015/anat/sub-03_ses-015_scout.json | 542 ++++++++++++++++++ .../ses-015/anat/sub-03_ses-015_scout.nii.gz | 1 + ...5_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-015_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...15_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...015_task-mario3_run-01_part-mag_events.tsv | 1 + ...015_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...15_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-01_part-phase_events.tsv | 1 + ...5_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-015_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...15_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...015_task-mario3_run-02_part-mag_events.tsv | 1 + ...015_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...15_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-02_part-phase_events.tsv | 1 + ...5_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-015_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...15_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...015_task-mario3_run-03_part-mag_events.tsv | 1 + ...015_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...15_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-03_part-phase_events.tsv | 1 + ...5_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-015_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...15_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...015_task-mario3_run-04_part-mag_events.tsv | 1 + ...015_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...15_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-04_part-phase_events.tsv | 1 + ...5_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-03/ses-015/sub-03_ses-015_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5409 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-015/anat/sub-03_ses-015_acq-axial_localizer.json create mode 120000 sub-03/ses-015/anat/sub-03_ses-015_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-015/anat/sub-03_ses-015_acq-coronal_localizer.json create mode 120000 sub-03/ses-015/anat/sub-03_ses-015_acq-coronal_localizer.nii.gz create mode 100644 sub-03/ses-015/anat/sub-03_ses-015_acq-sagittal_localizer.json create mode 120000 sub-03/ses-015/anat/sub-03_ses-015_acq-sagittal_localizer.nii.gz create mode 100644 sub-03/ses-015/anat/sub-03_ses-015_scout.json create mode 120000 sub-03/ses-015/anat/sub-03_ses-015_scout.nii.gz create mode 100644 sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-phase_sbref.nii.gz create mode 120000 sub-03/ses-015/sub-03_ses-015_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index f128bb082..e64b11f1f 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit f128bb082cb9d920dbfe7aeacde4a2acb3b7a9d1 +Subproject commit e64b11f1f4cd9b102757b97082f222d64f5eb371 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-03/ses-015/anat/sub-03_ses-015_acq-axial_localizer.json b/sub-03/ses-015/anat/sub-03_ses-015_acq-axial_localizer.json new file mode 100644 index 000000000..a4ee01d40 --- /dev/null +++ b/sub-03/ses-015/anat/sub-03_ses-015_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:01:18.057500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0383518, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 234.167 +} \ No newline at end of file diff --git a/sub-03/ses-015/anat/sub-03_ses-015_acq-axial_localizer.nii.gz b/sub-03/ses-015/anat/sub-03_ses-015_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..7df2d6c66 --- /dev/null +++ b/sub-03/ses-015/anat/sub-03_ses-015_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ 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"a9d27a99-9a7f-4760-91ab-53eda79cabfb||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-phase_sbref.nii.gz b/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-phase_sbref.nii.gz new file mode 120000 index 000000000..8d537d394 --- /dev/null +++ b/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Z7/GJ/MD5E-s1103563--7619f56b00eef68cb7658dd0e997e1d2.nii.gz/MD5E-s1103563--7619f56b00eef68cb7658dd0e997e1d2.nii.gz \ No newline at end of file diff --git a/sub-03/ses-015/sub-03_ses-015_scans.tsv b/sub-03/ses-015/sub-03_ses-015_scans.tsv new file mode 120000 index 000000000..1ecce5edd --- /dev/null +++ b/sub-03/ses-015/sub-03_ses-015_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/Qg/Qf/MD5E-s3289--56529bf1e88882eb864ea3c0ffed2f16.tsv/MD5E-s3289--56529bf1e88882eb864ea3c0ffed2f16.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..bc8d91e7d --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999909, 0.0020059, -0.0133584, -0.0055846, 0.961829, -0.273593], + "ImageOrientationText": "Tra>Cor(-15.9)>Sag(-0.7)", + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0564883, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [602, -7219, -8777, 689, 27, 10, 34, -18], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 234.167, + "dcmmeta_affine": [ + [-1.9998174905776978, -0.011169209145009518, -0.02459939382970333, 110.04737854003906], + [-0.0040117911994457245, 1.9236586093902588, -0.5472856163978577, -73.24537658691406], + [-0.026716792955994606, 0.5471863746643066, 1.923505425453186, -53.760643005371094], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 1ad743abc0c47badfab0e52a85559f4b6344749e Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:31:31 -0400 Subject: [PATCH 350/463] fill IntendedFor --- ...3_ses-018_acq-sbref_dir-AP_run-01_epi.json | 93 +++---------------- ...3_ses-018_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...3_ses-018_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...3_ses-018_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...3_ses-018_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- ...3_ses-018_acq-sbref_dir-PA_run-05_epi.json | 88 ++---------------- ...3_ses-018_acq-sbref_dir-PA_run-06_epi.json | 88 ++---------------- 7 files changed, 54 insertions(+), 567 deletions(-) diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_epi.json index a7a1103e4..06d30152f 100644 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999258, - 0.0303676, - 0.0236755, - -0.0228508, - 0.962543, - -0.270165 - ], + "ImageOrientationPatientDICOM": [0.999258, 0.0303676, 0.0236755, -0.0228508, 0.962543, -0.270165], "ImageOrientationText": "Tra>Cor(-15.6)>Sag(1.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,20 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-03_ses-018_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-018/func/sub-03_ses-018_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-018/func/sub-03_ses-018_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-018/func/sub-03_ses-018_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-018/func/sub-03_ses-018_task-mario3_run-05_part-mag_bold.nii.gz", + "ses-018/func/sub-03_ses-018_task-mario3_run-06_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +68,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 627, - -7201, - -8753, - 691, - 75, - 50, - 40, - -19 - ], + "ShimSetting": [627, -7201, -8753, 691, 75, 50, 40, -19], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.51, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.02, 4.1175, 4.215, 4.3125, 4.41, 4.51, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_epi.json index 7f53b5168..a1c7a7b79 100644 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999258, - 0.0303676, - 0.0236755, - -0.0228508, - 0.962543, - -0.270165 - ], + "ImageOrientationPatientDICOM": [0.999258, 0.0303676, 0.0236755, -0.0228508, 0.962543, -0.270165], "ImageOrientationText": "Tra>Cor(-15.6)>Sag(1.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-03_ses-018_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 627, - -7201, - -8753, - 691, - 75, - 50, - 40, - -19 - ], + "ShimSetting": [627, -7201, -8753, 691, 75, 50, 40, -19], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_epi.json index 6f86214f1..f027875b2 100644 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999258, - 0.0303676, - 0.0236755, - -0.0228508, - 0.962543, - -0.270165 - ], + "ImageOrientationPatientDICOM": [0.999258, 0.0303676, 0.0236755, -0.0228508, 0.962543, -0.270165], "ImageOrientationText": "Tra>Cor(-15.6)>Sag(1.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-03_ses-018_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 627, - -7201, - -8753, - 691, - 75, - 50, - 40, - -19 - ], + "ShimSetting": [627, -7201, -8753, 691, 75, 50, 40, -19], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_epi.json index b3328c875..96cc5128a 100644 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999258, - 0.0303676, - 0.0236755, - -0.0228508, - 0.962543, - -0.270165 - ], + "ImageOrientationPatientDICOM": [0.999258, 0.0303676, 0.0236755, -0.0228508, 0.962543, -0.270165], "ImageOrientationText": "Tra>Cor(-15.6)>Sag(1.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-03_ses-018_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 627, - -7201, - -8753, - 691, - 75, - 50, - 40, - -19 - ], + "ShimSetting": [627, -7201, -8753, 691, 75, 50, 40, -19], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_epi.json index 9c3c094c3..34d9479cf 100644 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999258, - 0.0303676, - 0.0236755, - -0.0228508, - 0.962543, - -0.270165 - ], + "ImageOrientationPatientDICOM": [0.999258, 0.0303676, 0.0236755, -0.0228508, 0.962543, -0.270165], "ImageOrientationText": "Tra>Cor(-15.6)>Sag(1.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-03_ses-018_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 627, - -7201, - -8753, - 691, - 75, - 50, - 40, - -19 - ], + "ShimSetting": [627, -7201, -8753, 691, 75, 50, 40, -19], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_epi.json index 339e54e26..b6d57522a 100644 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999258, - 0.0303676, - 0.0236755, - -0.0228508, - 0.962543, - -0.270165 - ], + "ImageOrientationPatientDICOM": [0.999258, 0.0303676, 0.0236755, -0.0228508, 0.962543, -0.270165], "ImageOrientationText": "Tra>Cor(-15.6)>Sag(1.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-03_ses-018_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 627, - -7201, - -8753, - 691, - 75, - 50, - 40, - -19 - ], + "ShimSetting": [627, -7201, -8753, 691, 75, 50, 40, -19], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_epi.json b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_epi.json index 39ec3f4fe..a81c90ed2 100644 --- a/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_epi.json +++ b/sub-03/ses-018/fmap/sub-03_ses-018_acq-sbref_dir-PA_run-06_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999258, - 0.0303676, - 0.0236755, - -0.0228508, - 0.962543, - -0.270165 - ], + "ImageOrientationPatientDICOM": [0.999258, 0.0303676, 0.0236755, -0.0228508, 0.962543, -0.270165], "ImageOrientationText": "Tra>Cor(-15.6)>Sag(1.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-03_ses-018_task-mario3_run-06_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-06_SBRef", "SeriesNumber": 24, - "ShimSetting": [ - 627, - -7201, - -8753, - 691, - 75, - 50, - 40, - -19 - ], + "ShimSetting": [627, -7201, -8753, 691, 75, 50, 40, -19], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 95bc0d529eda4bcbac9313d1fccd7e7428b0aed8 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:31:48 -0400 Subject: [PATCH 351/463] fix fmap phase --- ...3_ses-015_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-015_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-015_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-015_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-015_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-015_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-015_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-03/ses-015/sub-03_ses-015_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-03/ses-015/fmap/{sub-03_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-015_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-015/fmap/{sub-03_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-015_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-015/fmap/{sub-03_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-015_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-015/fmap/{sub-03_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-015_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-015/fmap/{sub-03_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-015_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-015/fmap/{sub-03_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-015_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-015/fmap/{sub-03_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-015_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-015/fmap/{sub-03_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-015_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-03/ses-015/fmap/{sub-03_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-03_ses-015_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-03/ses-015/fmap/{sub-03_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-03_ses-015_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-03/ses-015/fmap/{sub-03_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-03_ses-015_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-03/ses-015/fmap/{sub-03_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-03_ses-015_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 16005d1e6..000000000 --- a/sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:02:20.542500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999909, 0.0020059, -0.0133584, -0.0055846, 0.961829, -0.273593], - "ImageOrientationText": "Tra>Cor(-15.9)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0450497, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [602, -7219, -8777, 689, 27, 10, 34, -18], - "SliceThickness": 2, - "SliceTiming": [0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 234.167, - "WipMemBlock": "8e170e5f-fda6-4512-b878-1f0745492d3f||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9998174905776978, -0.011169209145009518, -0.02459939382970333, 110.04737854003906], - [-0.0040117911994457245, 1.9236586093902588, -0.5472856163978577, -73.24537658691406], - 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b/sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 2b44fc41e..000000000 --- a/sub-03/ses-015/fmap/sub-03_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3V/65/MD5E-s3334802--bf592f24404748258a6eb38997452bce.nii.gz/MD5E-s3334802--bf592f24404748258a6eb38997452bce.nii.gz \ No newline at end of file diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index a69f3d42e..000000000 --- a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:02:10.112500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999909, - 0.0020059, - -0.0133584, - -0.0055846, - 0.961829, - -0.273593 - ], - "ImageOrientationText": "Tra>Cor(-15.9)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0450497, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 602, - -7219, - -8777, - 689, - 27, - 10, - 34, - -18 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 234.167, - "WipMemBlock": "8e170e5f-fda6-4512-b878-1f0745492d3f||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index c2fa267b0..000000000 --- a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/xv/F6/MD5E-s1112260--c4a811d3b2ec09629d2c23f082b953b6.nii.gz/MD5E-s1112260--c4a811d3b2ec09629d2c23f082b953b6.nii.gz \ No newline at end of file diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 2fe7426c5..000000000 --- a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:03:19.080000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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"%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0564883, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 602, - -7219, - -8777, - 689, - 27, - 10, - 34, - -18 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 234.167, - "WipMemBlock": "5cd6afe6-28b7-4b5f-ba51-9c102144c020||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 7e52fcce4..000000000 --- a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Q6/Fw/MD5E-s1103697--510c2e2e6cc0baf3cac848255d4e6dff.nii.gz/MD5E-s1103697--510c2e2e6cc0baf3cac848255d4e6dff.nii.gz \ No newline at end of file diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index a05a57665..000000000 --- a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:14:1.965000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999909, - 0.0020059, - -0.0133584, - -0.0055846, - 0.961829, - -0.273593 - ], - "ImageOrientationText": "Tra>Cor(-15.9)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0564883, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 602, - -7219, - -8777, - 689, - 27, - 10, - 34, - -18 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 234.167, - "WipMemBlock": "897b20a5-adb7-4231-b128-478d2adf901d||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 42314cb47..000000000 --- a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/XK/9w/MD5E-s1103690--770cfe9f868bec1aacbbdf9a8fd88597.nii.gz/MD5E-s1103690--770cfe9f868bec1aacbbdf9a8fd88597.nii.gz \ No newline at end of file diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 920a5fcff..000000000 --- a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:23:35.257500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999909, - 0.0020059, - -0.0133584, - -0.0055846, - 0.961829, - -0.273593 - ], - "ImageOrientationText": "Tra>Cor(-15.9)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0564883, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 602, - -7219, - -8777, - 689, - 27, - 10, - 34, - -18 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 234.167, - "WipMemBlock": "f6144489-8317-4682-9d9d-e4ed66f20556||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 767d6b610..000000000 --- a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/GM/MM/MD5E-s1103872--a520e04b1a8819363022062da34f1a57.nii.gz/MD5E-s1103872--a520e04b1a8819363022062da34f1a57.nii.gz \ No newline at end of file diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 17dbd370a..000000000 --- a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:33:8.212500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999909, - 0.0020059, - -0.0133584, - -0.0055846, - 0.961829, - -0.273593 - ], - "ImageOrientationText": "Tra>Cor(-15.9)>Sag(-0.7)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0564883, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 602, - -7219, - -8777, - 689, - 27, - 10, - 34, - -18 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 234.167, - "WipMemBlock": "a9d27a99-9a7f-4760-91ab-53eda79cabfb||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 8d537d394..000000000 --- a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Z7/GJ/MD5E-s1103563--7619f56b00eef68cb7658dd0e997e1d2.nii.gz/MD5E-s1103563--7619f56b00eef68cb7658dd0e997e1d2.nii.gz \ No newline at end of file diff --git a/sub-03/ses-015/sub-03_ses-015_scans.tsv b/sub-03/ses-015/sub-03_ses-015_scans.tsv index 1ecce5edd..662d7a90f 120000 --- a/sub-03/ses-015/sub-03_ses-015_scans.tsv +++ b/sub-03/ses-015/sub-03_ses-015_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/Qg/Qf/MD5E-s3289--56529bf1e88882eb864ea3c0ffed2f16.tsv/MD5E-s3289--56529bf1e88882eb864ea3c0ffed2f16.tsv \ No newline at end of file +../../.git/annex/objects/P7/MJ/MD5E-s2567--d0d09122e8505202985f81ce257ecbef.tsv/MD5E-s2567--d0d09122e8505202985f81ce257ecbef.tsv \ No newline at end of file From c007a60d8392c0cd52fc23f93a46e1b019a085fa Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:32:11 -0400 Subject: [PATCH 352/463] fix complex event files --- ...g_events.tsv => sub-03_ses-015_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-03_ses-015_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-03_ses-015_task-mario3_run-03_events.tsv} | 0 .../func/sub-03_ses-015_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-03_ses-015_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-03_ses-015_task-mario3_run-04_events.tsv} | 0 .../func/sub-03_ses-015_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-03_ses-015_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-03/ses-015/func/{sub-03_ses-015_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-015_task-mario3_run-01_events.tsv} (100%) rename sub-03/ses-015/func/{sub-03_ses-015_task-mario3_run-01_part-phase_events.tsv => sub-03_ses-015_task-mario3_run-02_events.tsv} (100%) rename sub-03/ses-015/func/{sub-03_ses-015_task-mario3_run-02_part-mag_events.tsv => sub-03_ses-015_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_part-phase_events.tsv rename sub-03/ses-015/func/{sub-03_ses-015_task-mario3_run-02_part-phase_events.tsv => sub-03_ses-015_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-02_events.tsv similarity index 100% rename from sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-01_part-phase_events.tsv rename to sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-02_events.tsv diff --git a/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-02_part-mag_events.tsv b/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_events.tsv similarity index 100% rename from sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-02_part-mag_events.tsv rename to sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_events.tsv diff --git a/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_part-mag_events.tsv b/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_part-phase_events.tsv b/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-02_part-phase_events.tsv b/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_events.tsv similarity index 100% rename from sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-02_part-phase_events.tsv rename to sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_events.tsv diff --git a/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-mag_events.tsv b/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-phase_events.tsv b/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-015/func/sub-03_ses-015_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From a457958d45ac078232d6d6eaf5b5e06423ba22f2 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:33:34 -0400 Subject: [PATCH 353/463] fill IntendedFor --- ...3_ses-015_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...3_ses-015_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...3_ses-015_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...3_ses-015_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...3_ses-015_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_epi.json index 886000d27..ee6c32b69 100644 --- a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999909, - 0.0020059, - -0.0133584, - -0.0055846, - 0.961829, - -0.273593 - ], + "ImageOrientationPatientDICOM": [0.999909, 0.0020059, -0.0133584, -0.0055846, 0.961829, -0.273593], "ImageOrientationText": "Tra>Cor(-15.9)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-03_ses-015_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-015/func/sub-03_ses-015_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-015/func/sub-03_ses-015_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-015/func/sub-03_ses-015_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 602, - -7219, - -8777, - 689, - 27, - 10, - 34, - -18 - ], + "ShimSetting": [602, -7219, -8777, 689, 27, 10, 34, -18], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_epi.json b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_epi.json index 0f3df3bf7..bdb7b85c1 100644 --- a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999909, - 0.0020059, - -0.0133584, - -0.0055846, - 0.961829, - -0.273593 - ], + "ImageOrientationPatientDICOM": [0.999909, 0.0020059, -0.0133584, -0.0055846, 0.961829, -0.273593], "ImageOrientationText": "Tra>Cor(-15.9)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-03_ses-015_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 602, - -7219, - -8777, - 689, - 27, - 10, - 34, - -18 - ], + "ShimSetting": [602, -7219, -8777, 689, 27, 10, 34, -18], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_epi.json b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_epi.json index 4db58a93f..09865b1f6 100644 --- a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999909, - 0.0020059, - -0.0133584, - -0.0055846, - 0.961829, - -0.273593 - ], + "ImageOrientationPatientDICOM": [0.999909, 0.0020059, -0.0133584, -0.0055846, 0.961829, -0.273593], "ImageOrientationText": "Tra>Cor(-15.9)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-03_ses-015_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 602, - -7219, - -8777, - 689, - 27, - 10, - 34, - -18 - ], + "ShimSetting": [602, -7219, -8777, 689, 27, 10, 34, -18], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_epi.json b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_epi.json index e1454b410..e93f8ab97 100644 --- a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999909, - 0.0020059, - -0.0133584, - -0.0055846, - 0.961829, - -0.273593 - ], + "ImageOrientationPatientDICOM": [0.999909, 0.0020059, -0.0133584, -0.0055846, 0.961829, -0.273593], "ImageOrientationText": "Tra>Cor(-15.9)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-03_ses-015_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 602, - -7219, - -8777, - 689, - 27, - 10, - 34, - -18 - ], + "ShimSetting": [602, -7219, -8777, 689, 27, 10, 34, -18], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_epi.json b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_epi.json index 67ae95a43..34049d5ea 100644 --- a/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-03/ses-015/fmap/sub-03_ses-015_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999909, - 0.0020059, - -0.0133584, - -0.0055846, - 0.961829, - -0.273593 - ], + "ImageOrientationPatientDICOM": [0.999909, 0.0020059, -0.0133584, -0.0055846, 0.961829, -0.273593], "ImageOrientationText": "Tra>Cor(-15.9)>Sag(-0.7)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-03_ses-015_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 602, - -7219, - -8777, - 689, - 27, - 10, - 34, - -18 - ], + "ShimSetting": [602, -7219, -8777, 689, 27, 10, 34, -18], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 4cdf85f4e87a858938ebca0ebdf9a8284eaf96c7 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:38:16 -0400 Subject: [PATCH 354/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..e567b9bde --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = f1632ff1-1d0b-424c-b4a6-37b9063ccdc2 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..5a2fc1c6a --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 5a2fc1c6a7ffe0002ed2d00ddea98be0c63fa554 From b7a930394a2d2bedf05b1cf62a8283c862a50ab4 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:39:03 -0400 Subject: [PATCH 355/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-06_ses-015_acq-axial_localizer.json | 81 +++ .../sub-06_ses-015_acq-axial_localizer.nii.gz | 1 + .../sub-06_ses-015_acq-coronal_localizer.json | 81 +++ ...ub-06_ses-015_acq-coronal_localizer.nii.gz | 1 + ...sub-06_ses-015_acq-sagittal_localizer.json | 86 +++ ...b-06_ses-015_acq-sagittal_localizer.nii.gz | 1 + sub-06/ses-015/anat/sub-06_ses-015_scout.json | 542 ++++++++++++++++++ .../ses-015/anat/sub-06_ses-015_scout.nii.gz | 1 + ...5_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-015_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...15_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...015_task-mario3_run-01_part-mag_events.tsv | 1 + ...015_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...15_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-01_part-phase_events.tsv | 1 + ...5_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-015_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...15_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...015_task-mario3_run-02_part-mag_events.tsv | 1 + ...015_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...15_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-02_part-phase_events.tsv | 1 + ...5_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-015_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...15_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...015_task-mario3_run-03_part-mag_events.tsv | 1 + ...015_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...15_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-03_part-phase_events.tsv | 1 + ...5_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-015_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...15_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...015_task-mario3_run-04_part-mag_events.tsv | 1 + ...015_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...15_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-04_part-phase_events.tsv | 1 + ...5_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-06/ses-015/sub-06_ses-015_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5409 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-06/ses-015/anat/sub-06_ses-015_acq-axial_localizer.json create mode 120000 sub-06/ses-015/anat/sub-06_ses-015_acq-axial_localizer.nii.gz create mode 100644 sub-06/ses-015/anat/sub-06_ses-015_acq-coronal_localizer.json create mode 120000 sub-06/ses-015/anat/sub-06_ses-015_acq-coronal_localizer.nii.gz create mode 100644 sub-06/ses-015/anat/sub-06_ses-015_acq-sagittal_localizer.json create mode 120000 sub-06/ses-015/anat/sub-06_ses-015_acq-sagittal_localizer.nii.gz create mode 100644 sub-06/ses-015/anat/sub-06_ses-015_scout.json create mode 120000 sub-06/ses-015/anat/sub-06_ses-015_scout.nii.gz create mode 100644 sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_part-phase_sbref.nii.gz create mode 120000 sub-06/ses-015/sub-06_ses-015_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 5a2fc1c6a..edc912838 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 5a2fc1c6a7ffe0002ed2d00ddea98be0c63fa554 +Subproject commit edc91283894f38e63513968c23af2009187155b5 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..db37a3f34 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-06 41 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-06/ses-015/anat/sub-06_ses-015_acq-axial_localizer.json b/sub-06/ses-015/anat/sub-06_ses-015_acq-axial_localizer.json new file mode 100644 index 000000000..95a13a413 --- /dev/null +++ b/sub-06/ses-015/anat/sub-06_ses-015_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:42:30.037500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.032391, + "ScanningSequence": "GR", + 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May 2023 17:39:23 -0400 Subject: [PATCH 356/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..9546a92ae --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = dfd0dafe-e2ed-42d3-80cc-ac92e4ba83ed diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..c0fbb3bb5 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit c0fbb3bb558b9d12bc1144703d3434b6ae374d8f From fbae1fe5d1c081bdcddd01281d18f2a694c1b86a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:40:11 -0400 Subject: [PATCH 357/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-06_ses-013_acq-axial_localizer.json | 81 +++ .../sub-06_ses-013_acq-axial_localizer.nii.gz | 1 + .../sub-06_ses-013_acq-coronal_localizer.json | 81 +++ ...ub-06_ses-013_acq-coronal_localizer.nii.gz | 1 + ...sub-06_ses-013_acq-sagittal_localizer.json | 86 +++ ...b-06_ses-013_acq-sagittal_localizer.nii.gz | 1 + sub-06/ses-013/anat/sub-06_ses-013_scout.json | 542 ++++++++++++++++++ .../ses-013/anat/sub-06_ses-013_scout.nii.gz | 1 + ...3_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-013_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...13_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...013_task-mario3_run-01_part-mag_events.tsv | 1 + ...013_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...13_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-01_part-phase_events.tsv | 1 + ...3_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-013_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...13_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...013_task-mario3_run-02_part-mag_events.tsv | 1 + ...013_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...13_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-02_part-phase_events.tsv | 1 + ...3_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-013_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...13_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...013_task-mario3_run-03_part-mag_events.tsv | 1 + ...013_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...13_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-03_part-phase_events.tsv | 1 + ...3_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-06/ses-013/sub-06_ses-013_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 65 files changed, 4447 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-06/ses-013/anat/sub-06_ses-013_acq-axial_localizer.json create mode 120000 sub-06/ses-013/anat/sub-06_ses-013_acq-axial_localizer.nii.gz create mode 100644 sub-06/ses-013/anat/sub-06_ses-013_acq-coronal_localizer.json create mode 120000 sub-06/ses-013/anat/sub-06_ses-013_acq-coronal_localizer.nii.gz create mode 100644 sub-06/ses-013/anat/sub-06_ses-013_acq-sagittal_localizer.json create mode 120000 sub-06/ses-013/anat/sub-06_ses-013_acq-sagittal_localizer.nii.gz create mode 100644 sub-06/ses-013/anat/sub-06_ses-013_scout.json create mode 120000 sub-06/ses-013/anat/sub-06_ses-013_scout.nii.gz create mode 100644 sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-06/ses-013/sub-06_ses-013_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index c0fbb3bb5..7cd4f1cc5 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit c0fbb3bb558b9d12bc1144703d3434b6ae374d8f +Subproject commit 7cd4f1cc50b98339391b6d791680605f5176dd5f diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..db37a3f34 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-06 41 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-06/ses-013/anat/sub-06_ses-013_acq-axial_localizer.json b/sub-06/ses-013/anat/sub-06_ses-013_acq-axial_localizer.json new file mode 100644 index 000000000..67669a82e --- /dev/null +++ b/sub-06/ses-013/anat/sub-06_ses-013_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:42:32.070000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0270824, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 227.25 +} \ No newline at end of file diff --git a/sub-06/ses-013/anat/sub-06_ses-013_acq-axial_localizer.nii.gz b/sub-06/ses-013/anat/sub-06_ses-013_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..f2768e236 --- /dev/null +++ b/sub-06/ses-013/anat/sub-06_ses-013_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/2m/37/MD5E-s168189--adfe1af37d7447a6497479546d04fb70.nii.gz/MD5E-s168189--adfe1af37d7447a6497479546d04fb70.nii.gz \ No newline at end of file diff --git a/sub-06/ses-013/anat/sub-06_ses-013_acq-coronal_localizer.json b/sub-06/ses-013/anat/sub-06_ses-013_acq-coronal_localizer.json new file mode 100644 index 000000000..8fa455cbb --- /dev/null +++ b/sub-06/ses-013/anat/sub-06_ses-013_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:42:39.060000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "i", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0270824, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 227.25 +} \ No newline at end of file diff --git a/sub-06/ses-013/anat/sub-06_ses-013_acq-coronal_localizer.nii.gz b/sub-06/ses-013/anat/sub-06_ses-013_acq-coronal_localizer.nii.gz new file mode 120000 index 000000000..21e661b39 --- /dev/null +++ b/sub-06/ses-013/anat/sub-06_ses-013_acq-coronal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/33/KG/MD5E-s193668--29239afc4e811db168adaab68dd23e71.nii.gz/MD5E-s193668--29239afc4e811db168adaab68dd23e71.nii.gz \ No newline at end of file diff --git a/sub-06/ses-013/anat/sub-06_ses-013_acq-sagittal_localizer.json b/sub-06/ses-013/anat/sub-06_ses-013_acq-sagittal_localizer.json new file mode 100644 index 000000000..f6f9e7958 --- /dev/null +++ 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"ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [630, -7272, -8825, 509, -6, -206, -67, -15], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 227.25, + "dcmmeta_affine": [ + [-1.997629165649414, 0.09595312178134918, -0.016459424048662186, 102.44859313964844], + [0.0958326905965805, 1.878539800643921, -0.6796355843544006, -70.59066009521484], + [0.01714673824608326, 0.6796185970306396, 1.8809105157852173, -63.92596435546875], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 5966d86750b28b3ca4c92d8b5f3bef8b793c7dc9 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:40:28 -0400 Subject: [PATCH 358/463] fix fmap phase --- ...6_ses-015_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-015_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-015_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-015_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-015_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-015_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-015_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-06/ses-015/sub-06_ses-015_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-06/ses-015/fmap/{sub-06_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-06_ses-015_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-015/fmap/{sub-06_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-015_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-015/fmap/{sub-06_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-06_ses-015_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-015/fmap/{sub-06_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-015_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-015/fmap/{sub-06_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-06_ses-015_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-06/ses-015/fmap/{sub-06_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-06_ses-015_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-06/ses-015/fmap/{sub-06_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-06_ses-015_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-06/ses-015/fmap/{sub-06_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-06_ses-015_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-06/ses-015/fmap/{sub-06_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-06_ses-015_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-06/ses-015/fmap/{sub-06_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-06_ses-015_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-06/ses-015/fmap/{sub-06_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-06_ses-015_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-06/ses-015/fmap/{sub-06_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-06_ses-015_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 8aa03f2a2..000000000 --- a/sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:43:31.017500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999863, -0.0162979, 0.00277857, 0.0162308, 0.935636, -0.352592], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0380479, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [625, -7261, -8826, 521, 20, -189, -98, -6], - "SliceThickness": 2, - "SliceTiming": [0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 242.968, - "WipMemBlock": "ee7d891b-577c-47ba-bf5a-a2ad79b6c0e5||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.99972665309906, 0.03246157616376877, -0.0062935324385762215, 104.86327362060547], - [0.032595716416835785, 1.8712724447250366, -0.7051785588264465, -65.00753784179688], - [0.005557147320359945, 0.7051847577095032, 1.8715457916259766, -70.06279754638672], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99986332034195, -0.0162978576155, 0.00277857371971, 0.01623078855586, 0.93563623901671, -0.3525923846902], - "ImagePositionPatient": [-847.92332887451, -797.01187066715, 257.23568444692], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.25877, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "154138.941000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.03804788398351, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "154417.219000", - "SliceLocation": -42.971888609978, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000103803, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "154138.864000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["154331.017500", "154332.507500", "154333.997500"], - "ContentTime": ["154417.221000", "154417.224000", "154417.227000"], - "InstanceCreationTime": ["154417.221000", "154417.224000", "154417.227000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4788.0, 4816.0, 4790.0], - "WindowWidth": [18502.0, 18524.0, 18502.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 6572060d6..000000000 --- a/sub-06/ses-015/fmap/sub-06_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/wz/kx/MD5E-s3334383--1189261af74b0c5ea7eac05db8d08d4f.nii.gz/MD5E-s3334383--1189261af74b0c5ea7eac05db8d08d4f.nii.gz \ No newline at end of file diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 612567bac..000000000 --- a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:43:20.587500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0162979, - 0.00277857, - 0.0162308, - 0.935636, - -0.352592 - ], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0380479, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 625, - -7261, - -8826, - 521, - 20, - -189, - -98, - -6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 242.968, - "WipMemBlock": "ee7d891b-577c-47ba-bf5a-a2ad79b6c0e5||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 89337eb8d..000000000 --- a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/6p/K2/MD5E-s1112211--8bd6fae9252662534b3e43e73ef9533d.nii.gz/MD5E-s1112211--8bd6fae9252662534b3e43e73ef9533d.nii.gz \ No newline at end of file diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 5ecee74ed..000000000 --- a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:46:3.055000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0162979, - 0.00277857, - 0.0162308, - 0.935636, - -0.352592 - ], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - 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a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index e6ffc4392..000000000 --- a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/5v/Ff/MD5E-s1103534--b77e6f7435c62f5133fe0287a97d7721.nii.gz/MD5E-s1103534--b77e6f7435c62f5133fe0287a97d7721.nii.gz \ No newline at end of file diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index c702546c8..000000000 --- a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:54:57.985000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - 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a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/9v/ZM/MD5E-s1103442--cb57e4c80fd1a6a3bc82557c8140d329.nii.gz/MD5E-s1103442--cb57e4c80fd1a6a3bc82557c8140d329.nii.gz \ No newline at end of file diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 556f59620..000000000 --- a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:05:20.650000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": 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4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 242.968, - "WipMemBlock": "3dcdf65f-f449-4dcc-be32-4bf36230c6d5||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 44d2b6439..000000000 --- a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/M3/M4/MD5E-s1103509--905c430074df7d220f6aeb50e80c4aca.nii.gz/MD5E-s1103509--905c430074df7d220f6aeb50e80c4aca.nii.gz \ No newline at end of file diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 384796aad..000000000 --- a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:17:4.862500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0162979, - 0.00277857, - 0.0162308, - 0.935636, - -0.352592 - ], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0477087, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 625, - -7261, - -8826, - 521, - 20, - -189, - -98, - -6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 242.968, - "WipMemBlock": "ef775270-d399-41c9-88c7-221452fb2c51||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 886b5007d..000000000 --- a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3k/9K/MD5E-s1103437--64cedfd6f757572ccce18811da8424a1.nii.gz/MD5E-s1103437--64cedfd6f757572ccce18811da8424a1.nii.gz \ No newline at end of file diff --git a/sub-06/ses-015/sub-06_ses-015_scans.tsv b/sub-06/ses-015/sub-06_ses-015_scans.tsv index f85281286..bc54a6ed7 120000 --- a/sub-06/ses-015/sub-06_ses-015_scans.tsv +++ b/sub-06/ses-015/sub-06_ses-015_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/xp/50/MD5E-s3289--b90b06ff1905e5f9e22b3cf2bceec9e2.tsv/MD5E-s3289--b90b06ff1905e5f9e22b3cf2bceec9e2.tsv \ No newline at end of file +../../.git/annex/objects/Qq/Wv/MD5E-s2567--73cca6bc272ff7b57eb6ab48580aa22f.tsv/MD5E-s2567--73cca6bc272ff7b57eb6ab48580aa22f.tsv \ No newline at end of file From d9633c4ab0ebcc29c3ff97a222da42f89a077708 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:40:52 -0400 Subject: [PATCH 359/463] fix complex event files --- ...g_events.tsv => sub-06_ses-015_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-06_ses-015_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-06_ses-015_task-mario3_run-03_events.tsv} | 0 .../func/sub-06_ses-015_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-06_ses-015_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-06_ses-015_task-mario3_run-04_events.tsv} | 0 .../func/sub-06_ses-015_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-06_ses-015_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-06/ses-015/func/{sub-06_ses-015_task-mario3_run-01_part-mag_events.tsv => sub-06_ses-015_task-mario3_run-01_events.tsv} (100%) rename sub-06/ses-015/func/{sub-06_ses-015_task-mario3_run-01_part-phase_events.tsv => sub-06_ses-015_task-mario3_run-02_events.tsv} (100%) rename sub-06/ses-015/func/{sub-06_ses-015_task-mario3_run-02_part-mag_events.tsv => sub-06_ses-015_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_part-phase_events.tsv rename sub-06/ses-015/func/{sub-06_ses-015_task-mario3_run-02_part-phase_events.tsv => sub-06_ses-015_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_part-mag_events.tsv b/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_events.tsv similarity index 100% rename from sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_part-mag_events.tsv rename to sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_events.tsv diff --git a/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_part-phase_events.tsv b/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_events.tsv similarity index 100% rename from sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_part-phase_events.tsv rename to sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_events.tsv diff --git a/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_part-mag_events.tsv b/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_events.tsv similarity index 100% rename from sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_part-mag_events.tsv rename to sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_events.tsv diff --git a/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_part-mag_events.tsv b/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_part-phase_events.tsv b/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_part-phase_events.tsv b/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_events.tsv similarity index 100% rename from sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_part-phase_events.tsv rename to sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_events.tsv diff --git a/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_part-mag_events.tsv b/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_part-phase_events.tsv b/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From b6881da394691e7afca440cc87e7fc7a8812d722 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:41:18 -0400 Subject: [PATCH 360/463] fill IntendedFor --- ...6_ses-015_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...6_ses-015_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...6_ses-015_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...6_ses-015_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...6_ses-015_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_epi.json b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_epi.json index 2a38b3272..77b37cea3 100644 --- a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0162979, - 0.00277857, - 0.0162308, - 0.935636, - -0.352592 - ], + "ImageOrientationPatientDICOM": [0.999863, -0.0162979, 0.00277857, 0.0162308, 0.935636, -0.352592], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-06_ses-015_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-015/func/sub-06_ses-015_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-015/func/sub-06_ses-015_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-015/func/sub-06_ses-015_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 625, - -7261, - -8826, - 521, - 20, - -189, - -98, - -6 - ], + "ShimSetting": [625, -7261, -8826, 521, 20, -189, -98, -6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_epi.json b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_epi.json index fb5e10c42..c7bb2370f 100644 --- a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0162979, - 0.00277857, - 0.0162308, - 0.935636, - -0.352592 - ], + "ImageOrientationPatientDICOM": [0.999863, -0.0162979, 0.00277857, 0.0162308, 0.935636, -0.352592], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-06_ses-015_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 625, - -7261, - -8826, - 521, - 20, - -189, - -98, - -6 - ], + "ShimSetting": [625, -7261, -8826, 521, 20, -189, -98, -6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.51, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.02, 4.1175, 4.215, 4.3125, 4.41, 4.51, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_epi.json b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_epi.json index af8b0b69a..228c00f65 100644 --- a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0162979, - 0.00277857, - 0.0162308, - 0.935636, - -0.352592 - ], + "ImageOrientationPatientDICOM": [0.999863, -0.0162979, 0.00277857, 0.0162308, 0.935636, -0.352592], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-06_ses-015_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 625, - -7261, - -8826, - 521, - 20, - -189, - -98, - -6 - ], + "ShimSetting": [625, -7261, -8826, 521, 20, -189, -98, -6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_epi.json b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_epi.json index dde832980..c61e8985f 100644 --- a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0162979, - 0.00277857, - 0.0162308, - 0.935636, - -0.352592 - ], + "ImageOrientationPatientDICOM": [0.999863, -0.0162979, 0.00277857, 0.0162308, 0.935636, -0.352592], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-06_ses-015_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 625, - -7261, - -8826, - 521, - 20, - -189, - -98, - -6 - ], + "ShimSetting": [625, -7261, -8826, 521, 20, -189, -98, -6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_epi.json b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_epi.json index f542e8ba2..c429c8df2 100644 --- a/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-06/ses-015/fmap/sub-06_ses-015_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0162979, - 0.00277857, - 0.0162308, - 0.935636, - -0.352592 - ], + "ImageOrientationPatientDICOM": [0.999863, -0.0162979, 0.00277857, 0.0162308, 0.935636, -0.352592], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(-0.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-06_ses-015_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 625, - -7261, - -8826, - 521, - 20, - -189, - -98, - -6 - ], + "ShimSetting": [625, -7261, -8826, 521, 20, -189, -98, -6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From b492bdecacd378a3851bb293f5681be55a228db1 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:41:34 -0400 Subject: [PATCH 361/463] fix fmap phase --- ...6_ses-013_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-013_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-013_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-013_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-013_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-013_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-013_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-013_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-013_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-013_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-06/ses-013/sub-06_ses-013_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-06/ses-013/fmap/{sub-06_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-06_ses-013_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-013/fmap/{sub-06_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-013_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-013/fmap/{sub-06_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-06_ses-013_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-013/fmap/{sub-06_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-013_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-013/fmap/{sub-06_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-06_ses-013_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-06/ses-013/fmap/{sub-06_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-06_ses-013_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-06/ses-013/fmap/{sub-06_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-06_ses-013_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-06/ses-013/fmap/{sub-06_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-06_ses-013_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-06/ses-013/fmap/{sub-06_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-06_ses-013_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-06/ses-013/fmap/{sub-06_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-06_ses-013_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 84034aa7b..000000000 --- a/sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:43:35.107500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.998815, -0.0479163, 0.00857337, 0.0479766, 0.93927, -0.339809], - "ImageOrientationText": "Tra>Cor(-19.9)>Sag(-0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0318122, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [630, -7272, -8825, 509, -6, -206, -67, -15], - "SliceThickness": 2, - "SliceTiming": [0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 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"AcquisitionTime": ["154335.107500", "154336.597500", "154338.087500"], - "ContentTime": ["154421.587000", "154421.590000", "154421.593000"], - "InstanceCreationTime": ["154421.587000", "154421.590000", "154421.593000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4742.0, 4766.0, 4744.0], - "WindowWidth": [18554.0, 18584.0, 18552.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 61b860982..000000000 --- a/sub-06/ses-013/fmap/sub-06_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/7m/JP/MD5E-s3333918--cf779883a12bac7788607ddcbd9b05dc.nii.gz/MD5E-s3333918--cf779883a12bac7788607ddcbd9b05dc.nii.gz \ No newline at end of file diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 657c3d5fc..000000000 --- a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:43:24.677500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998815, - -0.0479163, - 0.00857337, - 0.0479766, - 0.93927, - -0.339809 - ], - "ImageOrientationText": "Tra>Cor(-19.9)>Sag(-0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0318122, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 630, - -7272, - -8825, - 509, - -6, - -206, - -67, - -15 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 227.25, - "WipMemBlock": "3f5f4956-2033-4a87-b208-10b3b06b6c80||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 986bdb3f1..000000000 --- a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/xz/VF/MD5E-s1111945--0502a65b9c933849caeeb91482610028.nii.gz/MD5E-s1111945--0502a65b9c933849caeeb91482610028.nii.gz \ No newline at end of file diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index f00c91b01..000000000 --- a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:45:13.287500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998815, - -0.0479163, - 0.00857337, - 0.0479766, - 0.93927, - -0.339809 - ], - "ImageOrientationText": "Tra>Cor(-19.9)>Sag(-0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": 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- 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 227.25, - "WipMemBlock": "ff16ca15-eecd-404a-85c1-bfee0ac84bd9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 4774f873c..000000000 --- a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/GM/7J/MD5E-s1103584--03b06498e8cd1f2a8c1056dc07b58668.nii.gz/MD5E-s1103584--03b06498e8cd1f2a8c1056dc07b58668.nii.gz \ No newline at end of file diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index c8c2deea5..000000000 --- a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:57:3.297500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998815, - -0.0479163, - 0.00857337, - 0.0479766, - 0.93927, - -0.339809 - ], - "ImageOrientationText": "Tra>Cor(-19.9)>Sag(-0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0398897, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 630, - -7272, - -8825, - 509, - -6, - -206, - -67, - -15 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 227.25, - "WipMemBlock": "dcd6a33f-11aa-469f-8d5c-6a240be424e6||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 21f2d41e2..000000000 --- a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3j/zw/MD5E-s1103421--93c9fcd721cb927bc80915ac4bb50cfa.nii.gz/MD5E-s1103421--93c9fcd721cb927bc80915ac4bb50cfa.nii.gz \ No newline at end of file diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 8012ba95b..000000000 --- a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:07:55.752500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998815, - -0.0479163, - 0.00857337, - 0.0479766, - 0.93927, - -0.339809 - ], - "ImageOrientationText": "Tra>Cor(-19.9)>Sag(-0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0398897, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 630, - -7272, - -8825, - 509, - -6, - -206, - -67, - -15 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 227.25, - "WipMemBlock": "8c086080-2947-4895-9f4f-99559507e99d||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 0314e99be..000000000 --- a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/wW/XF/MD5E-s1103553--c849694dbb50b715a73dc3c807affb16.nii.gz/MD5E-s1103553--c849694dbb50b715a73dc3c807affb16.nii.gz \ No newline at end of file diff --git a/sub-06/ses-013/sub-06_ses-013_scans.tsv b/sub-06/ses-013/sub-06_ses-013_scans.tsv index 8643f6577..46ce7e5ff 120000 --- a/sub-06/ses-013/sub-06_ses-013_scans.tsv +++ b/sub-06/ses-013/sub-06_ses-013_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/fG/49/MD5E-s2667--a627d336f6dc8bb633785739a48a15fa.tsv/MD5E-s2667--a627d336f6dc8bb633785739a48a15fa.tsv \ No newline at end of file +../../.git/annex/objects/GZ/JM/MD5E-s2066--ec78f9e64f8ea11bef04fcf0a235370f.tsv/MD5E-s2066--ec78f9e64f8ea11bef04fcf0a235370f.tsv \ No newline at end of file From 44f06ff7af6ed632a1cb34c7fe033d3a478cd0f9 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:42:21 -0400 Subject: [PATCH 362/463] fix complex event files --- ...g_events.tsv => sub-06_ses-013_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-06_ses-013_task-mario3_run-02_events.tsv} | 0 .../func/sub-06_ses-013_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-06_ses-013_task-mario3_run-03_events.tsv} | 0 .../func/sub-06_ses-013_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-06_ses-013_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-06/ses-013/func/{sub-06_ses-013_task-mario3_run-01_part-mag_events.tsv => sub-06_ses-013_task-mario3_run-01_events.tsv} (100%) rename sub-06/ses-013/func/{sub-06_ses-013_task-mario3_run-01_part-phase_events.tsv => sub-06_ses-013_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-02_part-phase_events.tsv rename sub-06/ses-013/func/{sub-06_ses-013_task-mario3_run-02_part-mag_events.tsv => sub-06_ses-013_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-01_part-mag_events.tsv b/sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-01_events.tsv similarity index 100% rename from sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-01_part-mag_events.tsv rename to sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-01_events.tsv diff --git a/sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-01_part-phase_events.tsv b/sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-02_events.tsv similarity index 100% rename from sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-01_part-phase_events.tsv rename to sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-02_events.tsv diff --git a/sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-02_part-phase_events.tsv b/sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-02_part-mag_events.tsv b/sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_events.tsv similarity index 100% rename from sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-02_part-mag_events.tsv rename to sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_events.tsv diff --git a/sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_part-mag_events.tsv b/sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_part-phase_events.tsv b/sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-013/func/sub-06_ses-013_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From ad29a8a904002b8e5c3c0f95790db4d025b1cb87 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:42:38 -0400 Subject: [PATCH 363/463] fill IntendedFor --- ...6_ses-013_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...6_ses-013_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...6_ses-013_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...6_ses-013_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_epi.json b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_epi.json index ed2d50e9c..a80ea06d8 100644 --- a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998815, - -0.0479163, - 0.00857337, - 0.0479766, - 0.93927, - -0.339809 - ], + "ImageOrientationPatientDICOM": [0.998815, -0.0479163, 0.00857337, 0.0479766, 0.93927, -0.339809], "ImageOrientationText": "Tra>Cor(-19.9)>Sag(-0.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-013/func/sub-06_ses-013_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-013/func/sub-06_ses-013_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-013/func/sub-06_ses-013_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 630, - -7272, - -8825, - 509, - -6, - -206, - -67, - -15 - ], + "ShimSetting": [630, -7272, -8825, 509, -6, -206, -67, -15], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_epi.json b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_epi.json index ae0ef1ef7..09fa10dff 100644 --- a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998815, - -0.0479163, - 0.00857337, - 0.0479766, - 0.93927, - -0.339809 - ], + "ImageOrientationPatientDICOM": [0.998815, -0.0479163, 0.00857337, 0.0479766, 0.93927, -0.339809], "ImageOrientationText": "Tra>Cor(-19.9)>Sag(-0.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-013/func/sub-06_ses-013_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 630, - -7272, - -8825, - 509, - -6, - -206, - -67, - -15 - ], + "ShimSetting": [630, -7272, -8825, 509, -6, -206, -67, -15], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_epi.json b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_epi.json index c0427710d..a9320b088 100644 --- a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998815, - -0.0479163, - 0.00857337, - 0.0479766, - 0.93927, - -0.339809 - ], + "ImageOrientationPatientDICOM": [0.998815, -0.0479163, 0.00857337, 0.0479766, 0.93927, -0.339809], "ImageOrientationText": "Tra>Cor(-19.9)>Sag(-0.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-013/func/sub-06_ses-013_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 630, - -7272, - -8825, - 509, - -6, - -206, - -67, - -15 - ], + "ShimSetting": [630, -7272, -8825, 509, -6, -206, -67, -15], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_epi.json b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_epi.json index 7969f548e..2a575c983 100644 --- a/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-06/ses-013/fmap/sub-06_ses-013_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998815, - -0.0479163, - 0.00857337, - 0.0479766, - 0.93927, - -0.339809 - ], + "ImageOrientationPatientDICOM": [0.998815, -0.0479163, 0.00857337, 0.0479766, 0.93927, -0.339809], "ImageOrientationText": "Tra>Cor(-19.9)>Sag(-0.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-013/func/sub-06_ses-013_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 630, - -7272, - -8825, - 509, - -6, - -206, - -67, - -15 - ], + "ShimSetting": [630, -7272, -8825, 509, -6, -206, -67, -15], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 1e50e38c9ca45e2efc6daec5ac3fcc5cd9ea936c Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:42:59 -0400 Subject: [PATCH 364/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-05_ses-006_acq-axial_localizer.json | 81 +++ .../sub-05_ses-006_acq-axial_localizer.nii.gz | 1 + .../sub-05_ses-006_acq-coronal_localizer.json | 81 +++ ...ub-05_ses-006_acq-coronal_localizer.nii.gz | 1 + ...sub-05_ses-006_acq-sagittal_localizer.json | 86 +++ ...b-05_ses-006_acq-sagittal_localizer.nii.gz | 1 + sub-05/ses-006/anat/sub-05_ses-006_scout.json | 542 ++++++++++++++++++ .../ses-006/anat/sub-05_ses-006_scout.nii.gz | 1 + ...6_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-06_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-06_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-07_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-07_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-07_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-07_part-phase_epi.nii.gz | 1 + ...-006_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...06_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...006_task-mario3_run-01_part-mag_events.tsv | 1 + ...006_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-01_part-phase_events.tsv | 1 + ...6_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-006_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...06_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...006_task-mario3_run-02_part-mag_events.tsv | 1 + ...006_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-02_part-phase_events.tsv | 1 + ...6_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-006_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...06_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...006_task-mario3_run-03_part-mag_events.tsv | 1 + ...006_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-03_part-phase_events.tsv | 1 + ...6_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-006_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...06_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...006_task-mario3_run-04_part-mag_events.tsv | 1 + ...006_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-04_part-phase_events.tsv | 1 + ...6_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-006_task-mario3_run-05_part-mag_bold.json | 172 ++++++ ...06_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...006_task-mario3_run-05_part-mag_events.tsv | 1 + ...006_task-mario3_run-05_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-05_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-05_part-phase_events.tsv | 1 + ...6_task-mario3_run-05_part-phase_sbref.json | 153 +++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + ...-006_task-mario3_run-06_part-mag_bold.json | 172 ++++++ ...06_task-mario3_run-06_part-mag_bold.nii.gz | 1 + ...006_task-mario3_run-06_part-mag_events.tsv | 1 + ...006_task-mario3_run-06_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-06_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-06_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-06_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-06_part-phase_events.tsv | 1 + ...6_task-mario3_run-06_part-phase_sbref.json | 153 +++++ ...task-mario3_run-06_part-phase_sbref.nii.gz | 1 + ...-006_task-mario3_run-07_part-mag_bold.json | 172 ++++++ ...06_task-mario3_run-07_part-mag_bold.nii.gz | 1 + ...006_task-mario3_run-07_part-mag_events.tsv | 1 + ...006_task-mario3_run-07_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-07_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-07_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-07_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-07_part-phase_events.tsv | 1 + ...6_task-mario3_run-07_part-phase_sbref.json | 153 +++++ ...task-mario3_run-07_part-phase_sbref.nii.gz | 1 + sub-05/ses-006/sub-05_ses-006_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 121 files changed, 8295 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-05/ses-006/anat/sub-05_ses-006_acq-axial_localizer.json create mode 120000 sub-05/ses-006/anat/sub-05_ses-006_acq-axial_localizer.nii.gz create mode 100644 sub-05/ses-006/anat/sub-05_ses-006_acq-coronal_localizer.json create mode 120000 sub-05/ses-006/anat/sub-05_ses-006_acq-coronal_localizer.nii.gz create mode 100644 sub-05/ses-006/anat/sub-05_ses-006_acq-sagittal_localizer.json create mode 120000 sub-05/ses-006/anat/sub-05_ses-006_acq-sagittal_localizer.nii.gz create mode 100644 sub-05/ses-006/anat/sub-05_ses-006_scout.json create mode 120000 sub-05/ses-006/anat/sub-05_ses-006_scout.nii.gz create mode 100644 sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 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-0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..da8d4ae9f --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-05 50 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-05/ses-006/anat/sub-05_ses-006_acq-axial_localizer.json b/sub-05/ses-006/anat/sub-05_ses-006_acq-axial_localizer.json new file mode 100644 index 000000000..8ca7840e9 --- /dev/null +++ b/sub-05/ses-006/anat/sub-05_ses-006_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:39:13.062500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0581701, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 599, + -7229, + -9119, + -10, + 50, + -38, + -82, + 55 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 309.502 +} \ No newline at end of file diff --git a/sub-05/ses-006/anat/sub-05_ses-006_acq-axial_localizer.nii.gz b/sub-05/ses-006/anat/sub-05_ses-006_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..c180f38c7 --- /dev/null +++ b/sub-05/ses-006/anat/sub-05_ses-006_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/mm/21/MD5E-s177787--4b11d179e123bd461d5c8f26c935421f.nii.gz/MD5E-s177787--4b11d179e123bd461d5c8f26c935421f.nii.gz \ No newline at end of file diff --git a/sub-05/ses-006/anat/sub-05_ses-006_acq-coronal_localizer.json b/sub-05/ses-006/anat/sub-05_ses-006_acq-coronal_localizer.json new file mode 100644 index 000000000..cf87fd462 --- /dev/null +++ b/sub-05/ses-006/anat/sub-05_ses-006_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:39:20.052500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": 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"TxRefAmp": 309.502, + "dcmmeta_affine": [ + [-1.9995149374008179, 0.012214635498821735, 0.04231701418757439, 103.10347747802734], + [-0.00496314000338316, 1.8468290567398071, -0.7675923109054565, -67.98622131347656], + [0.04376407712697983, 0.7675111293792725, 1.8463507890701294, -64.58615112304688], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From fed7054438089a4089bdf49c34899e27cda6d50a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:43:02 -0400 Subject: [PATCH 365/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-05_ses-003_acq-axial_localizer.json | 81 +++ .../sub-05_ses-003_acq-axial_localizer.nii.gz | 1 + .../sub-05_ses-003_acq-coronal_localizer.json | 81 +++ ...ub-05_ses-003_acq-coronal_localizer.nii.gz | 1 + ...sub-05_ses-003_acq-sagittal_localizer.json | 86 +++ ...b-05_ses-003_acq-sagittal_localizer.nii.gz | 1 + sub-05/ses-003/anat/sub-05_ses-003_scout.json | 542 ++++++++++++++++++ .../ses-003/anat/sub-05_ses-003_scout.nii.gz | 1 + ...3_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-06_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-06_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-07_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-07_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-07_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-07_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-08_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-08_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-08_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-08_part-phase_epi.nii.gz | 1 + ...-003_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-01_part-mag_events.tsv | 1 + ...003_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-01_part-phase_events.tsv | 1 + ...3_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-003_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-02_part-mag_events.tsv | 1 + ...003_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-02_part-phase_events.tsv | 1 + ...3_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-003_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-03_part-mag_events.tsv | 1 + ...003_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-03_part-phase_events.tsv | 1 + ...3_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-003_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-04_part-mag_events.tsv | 1 + ...003_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-04_part-phase_events.tsv | 1 + ...3_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-003_task-mario3_run-05_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-05_part-mag_events.tsv | 1 + ...003_task-mario3_run-05_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-05_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-05_part-phase_events.tsv | 1 + ...3_task-mario3_run-05_part-phase_sbref.json | 153 +++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + ...-003_task-mario3_run-06_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-06_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-06_part-mag_events.tsv | 1 + ...003_task-mario3_run-06_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-06_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-06_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-06_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-06_part-phase_events.tsv | 1 + ...3_task-mario3_run-06_part-phase_sbref.json | 153 +++++ ...task-mario3_run-06_part-phase_sbref.nii.gz | 1 + ...-003_task-mario3_run-07_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-07_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-07_part-mag_events.tsv | 1 + ...003_task-mario3_run-07_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-07_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-07_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-07_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-07_part-phase_events.tsv | 1 + ...3_task-mario3_run-07_part-phase_sbref.json | 153 +++++ ...task-mario3_run-07_part-phase_sbref.nii.gz | 1 + ...-003_task-mario3_run-08_part-mag_bold.json | 172 ++++++ ...03_task-mario3_run-08_part-mag_bold.nii.gz | 1 + ...003_task-mario3_run-08_part-mag_events.tsv | 1 + ...003_task-mario3_run-08_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-08_part-mag_sbref.nii.gz | 1 + ...03_task-mario3_run-08_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-08_part-phase_bold.nii.gz | 1 + ...3_task-mario3_run-08_part-phase_events.tsv | 1 + ...3_task-mario3_run-08_part-phase_sbref.json | 153 +++++ ...task-mario3_run-08_part-phase_sbref.nii.gz | 1 + sub-05/ses-003/sub-05_ses-003_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 135 files changed, 9257 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-05/ses-003/anat/sub-05_ses-003_acq-axial_localizer.json create mode 120000 sub-05/ses-003/anat/sub-05_ses-003_acq-axial_localizer.nii.gz create mode 100644 sub-05/ses-003/anat/sub-05_ses-003_acq-coronal_localizer.json create mode 120000 sub-05/ses-003/anat/sub-05_ses-003_acq-coronal_localizer.nii.gz create mode 100644 sub-05/ses-003/anat/sub-05_ses-003_acq-sagittal_localizer.json create mode 120000 sub-05/ses-003/anat/sub-05_ses-003_acq-sagittal_localizer.nii.gz create mode 100644 sub-05/ses-003/anat/sub-05_ses-003_scout.json create mode 120000 sub-05/ses-003/anat/sub-05_ses-003_scout.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_part-mag_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_part-mag_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_part-phase_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_part-mag_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_part-phase_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_part-mag_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_part-mag_epi.nii.gz create mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_part-phase_epi.json create mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_part-phase_epi.nii.gz create mode 100644 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-04_part-mag_bold.json create mode 120000 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160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit f9a1a53d1406ebae682fc2c3018a630fd391c75d +Subproject commit ba04573abcd64a41a1957b57c4500c0d2646d898 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..da8d4ae9f --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-05 50 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-05/ses-003/anat/sub-05_ses-003_acq-axial_localizer.json b/sub-05/ses-003/anat/sub-05_ses-003_acq-axial_localizer.json new file mode 100644 index 000000000..ba86d0ac2 --- /dev/null +++ b/sub-05/ses-003/anat/sub-05_ses-003_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:25:25.032500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": 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b/sub-05/ses-003/anat/sub-05_ses-003_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:25:32.022500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, 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"TxRefAmp": 322.451, + "dcmmeta_affine": [ + [-1.9997256994247437, 0.03281054273247719, 0.0045358953066170216, 102.30154418945312], + [0.028869876638054848, 1.8608139753341675, -0.7324873805046082, -69.79436492919922], + [0.016236882656812668, 0.7323214411735535, 1.861032485961914, -63.09316635131836], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From c54cba8ce352ea0fb8aca514ade8746daeed4ca8 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:43:08 -0400 Subject: [PATCH 366/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-05_ses-007_acq-axial_localizer.json | 81 +++ .../sub-05_ses-007_acq-axial_localizer.nii.gz | 1 + .../sub-05_ses-007_acq-coronal_localizer.json | 81 +++ ...ub-05_ses-007_acq-coronal_localizer.nii.gz | 1 + ...sub-05_ses-007_acq-sagittal_localizer.json | 86 +++ ...b-05_ses-007_acq-sagittal_localizer.nii.gz | 1 + sub-05/ses-007/anat/sub-05_ses-007_scout.json | 542 ++++++++++++++++++ .../ses-007/anat/sub-05_ses-007_scout.nii.gz | 1 + ...7_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-06_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-06_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-07_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-07_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-07_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-07_part-phase_epi.nii.gz | 1 + ...-007_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...07_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...007_task-mario3_run-01_part-mag_events.tsv | 1 + ...007_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...07_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-01_part-phase_events.tsv | 1 + ...7_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-007_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...07_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...007_task-mario3_run-02_part-mag_events.tsv | 1 + ...007_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...07_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-02_part-phase_events.tsv | 1 + ...7_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-007_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...07_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...007_task-mario3_run-03_part-mag_events.tsv | 1 + ...007_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...07_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-03_part-phase_events.tsv | 1 + ...7_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-007_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...07_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...007_task-mario3_run-04_part-mag_events.tsv | 1 + ...007_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...07_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-04_part-phase_events.tsv | 1 + ...7_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-007_task-mario3_run-05_part-mag_bold.json | 172 ++++++ ...07_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...007_task-mario3_run-05_part-mag_events.tsv | 1 + ...007_task-mario3_run-05_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...07_task-mario3_run-05_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-05_part-phase_events.tsv | 1 + ...7_task-mario3_run-05_part-phase_sbref.json | 153 +++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + ...-007_task-mario3_run-06_part-mag_bold.json | 172 ++++++ ...07_task-mario3_run-06_part-mag_bold.nii.gz | 1 + ...007_task-mario3_run-06_part-mag_events.tsv | 1 + ...007_task-mario3_run-06_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-06_part-mag_sbref.nii.gz | 1 + ...07_task-mario3_run-06_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-06_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-06_part-phase_events.tsv | 1 + ...7_task-mario3_run-06_part-phase_sbref.json | 153 +++++ ...task-mario3_run-06_part-phase_sbref.nii.gz | 1 + ...-007_task-mario3_run-07_part-mag_bold.json | 172 ++++++ ...07_task-mario3_run-07_part-mag_bold.nii.gz | 1 + ...007_task-mario3_run-07_part-mag_events.tsv | 1 + ...007_task-mario3_run-07_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-07_part-mag_sbref.nii.gz | 1 + ...07_task-mario3_run-07_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-07_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-07_part-phase_events.tsv | 1 + ...7_task-mario3_run-07_part-phase_sbref.json | 153 +++++ ...task-mario3_run-07_part-phase_sbref.nii.gz | 1 + sub-05/ses-007/sub-05_ses-007_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 121 files changed, 8295 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-05/ses-007/anat/sub-05_ses-007_acq-axial_localizer.json create mode 120000 sub-05/ses-007/anat/sub-05_ses-007_acq-axial_localizer.nii.gz create mode 100644 sub-05/ses-007/anat/sub-05_ses-007_acq-coronal_localizer.json create mode 120000 sub-05/ses-007/anat/sub-05_ses-007_acq-coronal_localizer.nii.gz create mode 100644 sub-05/ses-007/anat/sub-05_ses-007_acq-sagittal_localizer.json create mode 120000 sub-05/ses-007/anat/sub-05_ses-007_acq-sagittal_localizer.nii.gz create mode 100644 sub-05/ses-007/anat/sub-05_ses-007_scout.json create mode 120000 sub-05/ses-007/anat/sub-05_ses-007_scout.nii.gz create mode 100644 sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 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a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..da8d4ae9f --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-05 50 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-05/ses-007/anat/sub-05_ses-007_acq-axial_localizer.json b/sub-05/ses-007/anat/sub-05_ses-007_acq-axial_localizer.json new file mode 100644 index 000000000..a2229a6f2 --- /dev/null +++ b/sub-05/ses-007/anat/sub-05_ses-007_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:50:18.085000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + 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"SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 252.799 +} \ No newline at end of file diff --git a/sub-05/ses-007/anat/sub-05_ses-007_acq-axial_localizer.nii.gz b/sub-05/ses-007/anat/sub-05_ses-007_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..ed66404ec --- /dev/null +++ b/sub-05/ses-007/anat/sub-05_ses-007_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Mz/Qz/MD5E-s179073--f004962bc1f2276c4252b3bfb6e79d12.nii.gz/MD5E-s179073--f004962bc1f2276c4252b3bfb6e79d12.nii.gz \ No newline at end of file diff --git a/sub-05/ses-007/anat/sub-05_ses-007_acq-coronal_localizer.json b/sub-05/ses-007/anat/sub-05_ses-007_acq-coronal_localizer.json new file mode 100644 index 000000000..bdbc55463 --- /dev/null +++ b/sub-05/ses-007/anat/sub-05_ses-007_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:50:25.075000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, 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b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-07_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/mj/Xj/MD5E-s1103567--ea8518c9cb11e4674e4854b7d13382db.nii.gz/MD5E-s1103567--ea8518c9cb11e4674e4854b7d13382db.nii.gz \ No newline at end of file diff --git a/sub-05/ses-007/sub-05_ses-007_scans.tsv b/sub-05/ses-007/sub-05_ses-007_scans.tsv new file mode 120000 index 000000000..b46a892e8 --- /dev/null +++ b/sub-05/ses-007/sub-05_ses-007_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/q5/7m/MD5E-s5155--3528bfe6849c7908205d5e13358825b8.tsv/MD5E-s5155--3528bfe6849c7908205d5e13358825b8.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..f2f232a3f --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999758, -0.0113229, 0.0188841, 0.0176254, 0.925581, -0.37814], + "ImageOrientationText": "Tra>Cor(-22.2)>Sag(0.8)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": 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"TxRefAmp": 252.799, + "dcmmeta_affine": [ + [-1.999515175819397, 0.035250816494226456, 0.02639419212937355, 101.39836883544922], + [0.022645890712738037, 1.8511611223220825, -0.7567625641822815, -69.7623062133789], + [0.037768200039863586, 0.756280243396759, 1.8511115312576294, -57.14202880859375], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 9b23d2c9fa6bb6b2897d7d27b7f0d7a0210e695c Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:44:16 -0400 Subject: [PATCH 367/463] fix fmap phase --- ...5_ses-006_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-006_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-006_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-06_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-06_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-07_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-07_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-07_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-07_part-phase_epi.nii.gz | 1 - sub-05/ses-006/sub-05_ses-006_scans.tsv | 2 +- 37 files changed, 1 insertion(+), 1403 deletions(-) rename sub-05/ses-006/fmap/{sub-05_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-05_ses-006_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-006/fmap/{sub-05_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-006_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-006/fmap/{sub-05_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-05_ses-006_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-006/fmap/{sub-05_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-006_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-006/fmap/{sub-05_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-05_ses-006_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-05/ses-006/fmap/{sub-05_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-05_ses-006_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-05/ses-006/fmap/{sub-05_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-05_ses-006_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-05/ses-006/fmap/{sub-05_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-05_ses-006_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-05/ses-006/fmap/{sub-05_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-05_ses-006_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-05/ses-006/fmap/{sub-05_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-05_ses-006_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-05/ses-006/fmap/{sub-05_ses-006_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-05_ses-006_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-05/ses-006/fmap/{sub-05_ses-006_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-05_ses-006_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-05/ses-006/fmap/{sub-05_ses-006_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-05_ses-006_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-05/ses-006/fmap/{sub-05_ses-006_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-05_ses-006_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz rename sub-05/ses-006/fmap/{sub-05_ses-006_acq-sbref_dir-PA_run-06_part-mag_epi.json => sub-05_ses-006_acq-sbref_dir-PA_run-06_epi.json} (100%) rename sub-05/ses-006/fmap/{sub-05_ses-006_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz => sub-05_ses-006_acq-sbref_dir-PA_run-06_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_part-phase_epi.json delete mode 120000 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz rename sub-05/ses-006/fmap/{sub-05_ses-006_acq-sbref_dir-PA_run-07_part-mag_epi.json => sub-05_ses-006_acq-sbref_dir-PA_run-07_epi.json} (100%) rename sub-05/ses-006/fmap/{sub-05_ses-006_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz => sub-05_ses-006_acq-sbref_dir-PA_run-07_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_part-phase_epi.json delete mode 120000 sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index f1863f307..000000000 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:40:20.190000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - 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"BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99975747970292, 0.00248156988835, 0.02188203804397, 0.00610731767702, 0.92341450962169, -0.3837555785796], - "ImagePositionPatient": [-836.61408809243, -796.31222440113, 277.87522966481], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.259129, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "183820.357000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.06832917222974, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "184106.492000", - "SliceLocation": -31.392482501341, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999903652, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "183820.284000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["184020.190000", "184021.680000", "184023.170000"], - "ContentTime": ["184106.494000", "184106.508000", "184106.511000"], - "InstanceCreationTime": ["184106.494000", "184106.508000", "184106.511000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4872.0, 4874.0, 4876.0], - "WindowWidth": [18674.0, 18672.0, 18670.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 055ab46a7..000000000 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Zm/J3/MD5E-s3334087--8d4568509ebf79123fc09c3558e57dfa.nii.gz/MD5E-s3334087--8d4568509ebf79123fc09c3558e57dfa.nii.gz \ No newline at end of file diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 77e26d4d7..000000000 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:40:9.760000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999757, - 0.00248157, - 0.021882, - 0.00610732, - 0.923415, - -0.383756 - ], - "ImageOrientationText": "Tra>Cor(-22.6)>Sag(1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0683292, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 587, - -7295, - -8810, - 404, - 24, - -362, - -45, - 96 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 309.502, - "WipMemBlock": "0692c7c8-5c8d-4d97-bb6e-59325db9a1da||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 97613a974..000000000 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/xx/97/MD5E-s1112322--f2a40221fec1147d26179f9ced222dbe.nii.gz/MD5E-s1112322--f2a40221fec1147d26179f9ced222dbe.nii.gz \ No newline at end of file diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index cb84faa8e..000000000 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:41:47.480000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999757, - 0.00248157, - 0.021882, - 0.00610732, - 0.923415, - -0.383756 - ], - "ImageOrientationText": "Tra>Cor(-22.6)>Sag(1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0856788, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 587, - -7295, - -8810, - 404, - 24, - -363, - -45, - 95 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 309.502, - "WipMemBlock": "1c2a2605-b6b1-4218-96c3-a17cd57bd3a4||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 34e36e1e1..000000000 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/gg/WG/MD5E-s1103439--5d9776d033ea0d47213fc61267068874.nii.gz/MD5E-s1103439--5d9776d033ea0d47213fc61267068874.nii.gz \ No newline at end of file diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 6738f07f5..000000000 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:54:10.542500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999757, - 0.00248157, - 0.021882, - 0.00610732, - 0.923415, - -0.383756 - ], - "ImageOrientationText": "Tra>Cor(-22.6)>Sag(1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0856788, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 587, - -7295, - -8810, - 404, - 24, - -363, - -45, - 95 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 309.502, - "WipMemBlock": "0dc31c9f-d2c5-4aa3-9137-7f83ba856201||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 64cc97aad..000000000 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/jG/3P/MD5E-s1103245--57c07950cc9ca5bbfdc917ce6c630430.nii.gz/MD5E-s1103245--57c07950cc9ca5bbfdc917ce6c630430.nii.gz \ No newline at end of file diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index ebc8a795a..000000000 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:05:15.232500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999757, - 0.00248157, - 0.021882, - 0.00610732, - 0.923415, - -0.383756 - ], - "ImageOrientationText": "Tra>Cor(-22.6)>Sag(1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0856788, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 587, - -7295, - -8810, - 404, - 24, - -363, - -45, - 95 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 309.502, - "WipMemBlock": "75c25f3a-bfa5-4b17-9bcb-c1ef1c44bf1b||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index d99fbfdd2..000000000 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Q1/49/MD5E-s1103490--0513ec40190f83a9ff481447b2829ff5.nii.gz/MD5E-s1103490--0513ec40190f83a9ff481447b2829ff5.nii.gz \ No newline at end of file diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 520c9538a..000000000 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:13:54.715000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999757, - 0.00248157, - 0.021882, - 0.00610732, - 0.923415, - -0.383756 - ], - "ImageOrientationText": "Tra>Cor(-22.6)>Sag(1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0856788, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 587, - -7295, - -8810, - 404, - 24, - -363, - -45, - 95 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 309.502, - "WipMemBlock": "6deba003-bbfc-4a0b-b9fb-887a989fbe81||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 03f7b1bb2..000000000 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/9p/37/MD5E-s1103674--2e6043950104b9da1e046d07efa5e332.nii.gz/MD5E-s1103674--2e6043950104b9da1e046d07efa5e332.nii.gz \ No newline at end of file diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index bad4b9b00..000000000 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:25:56.325000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999757, - 0.00248157, - 0.021882, - 0.00610732, - 0.923415, - -0.383756 - ], - "ImageOrientationText": "Tra>Cor(-22.6)>Sag(1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-05", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0856788, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 587, - -7295, - -8810, - 404, - 24, - -363, - -45, - 95 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 309.502, - "WipMemBlock": "2be07680-1e1e-4f81-9d31-3970b8437c8d||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index 6bf2ffa41..000000000 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/vJ/qx/MD5E-s1103531--cdd4c133d0682468d05303ba8c3ff934.nii.gz/MD5E-s1103531--cdd4c133d0682468d05303ba8c3ff934.nii.gz \ No newline at end of file diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_part-mag_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_epi.json similarity index 100% rename from sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_part-mag_epi.json rename to sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_epi.json diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_epi.nii.gz similarity index 100% rename from sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz rename to sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_epi.nii.gz diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_part-phase_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_part-phase_epi.json deleted file mode 100644 index 6a8a19194..000000000 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:35:21.047500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999757, - 0.00248157, - 0.021882, - 0.00610732, - 0.923415, - -0.383756 - ], - "ImageOrientationText": "Tra>Cor(-22.6)>Sag(1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-06", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0856788, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-06_SBRef", - "SeriesNumber": 24, - "ShimSetting": [ - 587, - -7295, - -8810, - 404, - 24, - -363, - -45, - 95 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 309.502, - "WipMemBlock": "3298d805-d2ed-43fe-9b61-713cbc939200||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz deleted file mode 120000 index a2c1f971c..000000000 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/9k/p4/MD5E-s1103543--22a3e254e9a8ef31aef16d643d001e61.nii.gz/MD5E-s1103543--22a3e254e9a8ef31aef16d643d001e61.nii.gz \ No newline at end of file diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_part-mag_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_epi.json similarity index 100% rename from sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_part-mag_epi.json rename to sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_epi.json diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_epi.nii.gz similarity index 100% rename from sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz rename to sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_epi.nii.gz diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_part-phase_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_part-phase_epi.json deleted file mode 100644 index 2924db614..000000000 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:47:45.345000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999757, - 0.00248157, - 0.021882, - 0.00610732, - 0.923415, - -0.383756 - ], - "ImageOrientationText": "Tra>Cor(-22.6)>Sag(1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-07", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0856788, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-07_SBRef", - "SeriesNumber": 27, - "ShimSetting": [ - 587, - -7295, - -8810, - 404, - 24, - -363, - -45, - 95 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 309.502, - "WipMemBlock": "2ca43df3-ae03-4dcb-a2e1-e1cf016a480f||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz deleted file mode 120000 index b967a875a..000000000 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/F8/6q/MD5E-s1103507--3f74aae5fc7bb420b89f5ec9556d604e.nii.gz/MD5E-s1103507--3f74aae5fc7bb420b89f5ec9556d604e.nii.gz \ No newline at end of file diff --git a/sub-05/ses-006/sub-05_ses-006_scans.tsv b/sub-05/ses-006/sub-05_ses-006_scans.tsv index caea51f81..0f1f40024 120000 --- a/sub-05/ses-006/sub-05_ses-006_scans.tsv +++ b/sub-05/ses-006/sub-05_ses-006_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/35/z5/MD5E-s5155--f9daef9571a861bfff684c30966f633f.tsv/MD5E-s5155--f9daef9571a861bfff684c30966f633f.tsv \ No newline at end of file +../../.git/annex/objects/Mk/FK/MD5E-s4070--5220fbf6f25ac7bb91be71db939cbd15.tsv/MD5E-s4070--5220fbf6f25ac7bb91be71db939cbd15.tsv \ No newline at end of file From 02bbdfa8b3130feddd38ad2616f69a27c8fcc588 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:44:17 -0400 Subject: [PATCH 368/463] fix fmap phase --- ...5_ses-003_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-003_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-003_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-06_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-06_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-07_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-07_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-07_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-07_part-phase_epi.nii.gz | 1 - ..._ses-003_acq-sbref_dir-PA_run-08_epi.json} | 0 ...es-003_acq-sbref_dir-PA_run-08_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-08_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-08_part-phase_epi.nii.gz | 1 - sub-05/ses-003/sub-05_ses-003_scans.tsv | 2 +- 41 files changed, 1 insertion(+), 1556 deletions(-) rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-05_ses-003_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-003_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-05_ses-003_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-003_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-05_ses-003_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-05_ses-003_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-05_ses-003_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-05_ses-003_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-05_ses-003_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-05_ses-003_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-05_ses-003_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-05_ses-003_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-05_ses-003_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-05_ses-003_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-sbref_dir-PA_run-06_part-mag_epi.json => sub-05_ses-003_acq-sbref_dir-PA_run-06_epi.json} (100%) rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz => sub-05_ses-003_acq-sbref_dir-PA_run-06_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_part-phase_epi.json delete mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-sbref_dir-PA_run-07_part-mag_epi.json => sub-05_ses-003_acq-sbref_dir-PA_run-07_epi.json} (100%) rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz => sub-05_ses-003_acq-sbref_dir-PA_run-07_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_part-phase_epi.json delete mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-sbref_dir-PA_run-08_part-mag_epi.json => sub-05_ses-003_acq-sbref_dir-PA_run-08_epi.json} (100%) rename sub-05/ses-003/fmap/{sub-05_ses-003_acq-sbref_dir-PA_run-08_part-mag_epi.nii.gz => sub-05_ses-003_acq-sbref_dir-PA_run-08_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_part-phase_epi.json delete mode 120000 sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_part-phase_epi.nii.gz diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index ba879e11a..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:26:56.727500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999863, -0.0144349, 0.00811844, 0.0164053, 0.930407, -0.366161], - "ImageOrientationText": "Tra>Cor(-21.5)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - 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"SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "182743.983000", - "SliceLocation": -32.915453156998, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000529304, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "182341.858000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["182656.727500", "182658.217500", "182659.707500"], - "ContentTime": ["182743.985000", "182743.987000", "182743.990000"], - "InstanceCreationTime": ["182743.985000", "182743.987000", "182743.990000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4818.0, 4812.0, 4816.0], - "WindowWidth": [18626.0, 18624.0, 18626.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index ee0ef7385..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Jv/jW/MD5E-s3333830--403d29146c305b7192e138b8ffe5ecf7.nii.gz/MD5E-s3333830--403d29146c305b7192e138b8ffe5ecf7.nii.gz \ No newline at end of file diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 9f5892bea..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:26:46.297500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - 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1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 322.451, - "WipMemBlock": "e5c82a89-36da-4e5d-ab4c-d6aec64d620e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 666c33e53..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/j9/Jz/MD5E-s1112155--7682f30c16c86375f181ed71fcd60ddb.nii.gz/MD5E-s1112155--7682f30c16c86375f181ed71fcd60ddb.nii.gz \ No newline at end of file diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 2d8552acd..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:28:37.242500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0144349, - 0.00811844, - 0.0164053, - 0.930407, - -0.366161 - ], - "ImageOrientationText": "Tra>Cor(-21.5)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0967074, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 599, - -7261, - -8811, - 450, - 13, - -363, - -8, - 32 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 322.451, - "WipMemBlock": "df8c61ba-1830-4b92-8ee8-3a3e25a7f2bc||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 029e14961..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/6Z/zk/MD5E-s1103360--2ef1b04c54a37e216585abeb357f2bd1.nii.gz/MD5E-s1103360--2ef1b04c54a37e216585abeb357f2bd1.nii.gz \ No newline at end of file diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index bb0a86aa6..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:39:35.635000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0144349, - 0.00811844, - 0.0164053, - 0.930407, - -0.366161 - ], - "ImageOrientationText": "Tra>Cor(-21.5)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0967074, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 599, - -7261, - -8811, - 450, - 13, - -363, - -8, - 32 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 322.451, - "WipMemBlock": "de01ba84-c060-450b-8dbf-6767c2fe9609||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 6ccd90196..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/0x/03/MD5E-s1103550--54eee795ae19e668e0d004234ae40f9f.nii.gz/MD5E-s1103550--54eee795ae19e668e0d004234ae40f9f.nii.gz \ No newline at end of file diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index ec8bbb691..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:49:24.067500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0144349, - 0.00811844, - 0.0164053, - 0.930407, - -0.366161 - ], - "ImageOrientationText": "Tra>Cor(-21.5)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0967074, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 599, - -7261, - -8811, - 450, - 13, - -363, - -8, - 32 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 322.451, - "WipMemBlock": "8ac269e8-7247-41c8-9674-cdce1263fad7||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 6cf57a26a..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/vw/k7/MD5E-s1103511--851388e94c0492b6a0ce81ff040b82b6.nii.gz/MD5E-s1103511--851388e94c0492b6a0ce81ff040b82b6.nii.gz \ No newline at end of file diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 72002f88b..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:04:12.860000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0144349, - 0.00811844, - 0.0164053, - 0.930407, - -0.366161 - ], - "ImageOrientationText": "Tra>Cor(-21.5)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0967074, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 599, - -7261, - -8811, - 450, - 13, - -363, - -8, - 32 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, 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a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/VZ/6p/MD5E-s1103568--df8c84c4ff35226c0c6c17f31213a0cf.nii.gz/MD5E-s1103568--df8c84c4ff35226c0c6c17f31213a0cf.nii.gz \ No newline at end of file diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index 214420916..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:14:5.110000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0144349, - 0.00811844, - 0.0164053, - 0.930407, - -0.366161 - ], - "ImageOrientationText": "Tra>Cor(-21.5)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-05", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0967074, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 599, - -7261, - -8811, - 450, - 13, - -363, - -8, - 32 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 322.451, - "WipMemBlock": "a29f2b55-0d46-4763-bfaf-427a97eb2389||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index aa484c7b0..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/vG/KZ/MD5E-s1103523--ccb275e57d73741287d57593cabe15a4.nii.gz/MD5E-s1103523--ccb275e57d73741287d57593cabe15a4.nii.gz \ No newline at end of file diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_part-mag_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_epi.json similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_part-mag_epi.json rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_epi.json diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_epi.nii.gz similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_epi.nii.gz diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_part-phase_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_part-phase_epi.json deleted file mode 100644 index 9526dbca7..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:23:59.960000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0144349, - 0.00811844, - 0.0164053, - 0.930407, - -0.366161 - ], - "ImageOrientationText": "Tra>Cor(-21.5)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-06", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0967074, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-06_SBRef", - "SeriesNumber": 24, - "ShimSetting": [ - 599, - -7261, - -8811, - 450, - 13, - -363, - -8, - 32 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 322.451, - "WipMemBlock": "c2c32abc-64fe-4872-bf04-e25bd767cf8c||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz deleted file mode 120000 index d19e83b22..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/1M/13/MD5E-s1103549--b7bde990b7fef70c0c863a9105551057.nii.gz/MD5E-s1103549--b7bde990b7fef70c0c863a9105551057.nii.gz \ No newline at end of file diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_part-mag_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_epi.json similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_part-mag_epi.json rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_epi.json diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_epi.nii.gz similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_epi.nii.gz diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_part-phase_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_part-phase_epi.json deleted file mode 100644 index 6e59bb4bc..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:34:43.985000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0144349, - 0.00811844, - 0.0164053, - 0.930407, - -0.366161 - ], - "ImageOrientationText": "Tra>Cor(-21.5)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-07", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0967074, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-07_SBRef", - "SeriesNumber": 27, - "ShimSetting": [ - 599, - -7261, - -8811, - 450, - 13, - -363, - -8, - 32 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 322.451, - "WipMemBlock": "778b4e39-cd22-4e5a-9e71-81e42fd805f7||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz deleted file mode 120000 index 12b1cc93d..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/ZJ/Jx/MD5E-s1103511--8d946a7cf7e0e052d599cc0b029209dd.nii.gz/MD5E-s1103511--8d946a7cf7e0e052d599cc0b029209dd.nii.gz \ No newline at end of file diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_part-mag_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_epi.json similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_part-mag_epi.json rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_epi.json diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_part-mag_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_epi.nii.gz similarity index 100% rename from sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_part-mag_epi.nii.gz rename to sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_epi.nii.gz diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_part-phase_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_part-phase_epi.json deleted file mode 100644 index f115e57e8..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:45:11.455000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0144349, - 0.00811844, - 0.0164053, - 0.930407, - -0.366161 - ], - "ImageOrientationText": "Tra>Cor(-21.5)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-08", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0967074, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-08_SBRef", - "SeriesNumber": 30, - "ShimSetting": [ - 599, - -7261, - -8811, - 450, - 13, - -363, - -8, - 32 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 322.451, - "WipMemBlock": "0cfb78f7-fd37-4ed3-8283-11ea08dd0781||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_part-phase_epi.nii.gz b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_part-phase_epi.nii.gz deleted file mode 120000 index 20143afbf..000000000 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/X2/1M/MD5E-s1103313--83299c29a8f3d092fcdbb74f0509b817.nii.gz/MD5E-s1103313--83299c29a8f3d092fcdbb74f0509b817.nii.gz \ No newline at end of file diff --git a/sub-05/ses-003/sub-05_ses-003_scans.tsv b/sub-05/ses-003/sub-05_ses-003_scans.tsv index 83f0d0732..da1a22688 120000 --- a/sub-05/ses-003/sub-05_ses-003_scans.tsv +++ b/sub-05/ses-003/sub-05_ses-003_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/6f/Xx/MD5E-s5777--aab844864da56bf32044e5bc7feb56c1.tsv/MD5E-s5777--aab844864da56bf32044e5bc7feb56c1.tsv \ No newline at end of file +../../.git/annex/objects/QK/3X/MD5E-s4571--0fb37735a62c03d95770161992400c8c.tsv/MD5E-s4571--0fb37735a62c03d95770161992400c8c.tsv \ No newline at end of file From 9afcbca13f3cf1ecf02c9aab5d4a0e9501c80f2e Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:44:19 -0400 Subject: [PATCH 369/463] fix fmap phase --- ...5_ses-007_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-007_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-007_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-007_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-007_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-007_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-007_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-007_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-PA_run-06_epi.json} | 0 ...es-007_acq-sbref_dir-PA_run-06_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 - ..._ses-007_acq-sbref_dir-PA_run-07_epi.json} | 0 ...es-007_acq-sbref_dir-PA_run-07_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-07_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-07_part-phase_epi.nii.gz | 1 - sub-05/ses-007/sub-05_ses-007_scans.tsv | 2 +- 37 files changed, 1 insertion(+), 1403 deletions(-) rename sub-05/ses-007/fmap/{sub-05_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-05_ses-007_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-007/fmap/{sub-05_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-007_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-007/fmap/{sub-05_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-05_ses-007_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-007/fmap/{sub-05_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-007_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-007/fmap/{sub-05_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-05_ses-007_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-05/ses-007/fmap/{sub-05_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-05_ses-007_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-05/ses-007/fmap/{sub-05_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-05_ses-007_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-05/ses-007/fmap/{sub-05_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-05_ses-007_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-05/ses-007/fmap/{sub-05_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-05_ses-007_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-05/ses-007/fmap/{sub-05_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-05_ses-007_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-05/ses-007/fmap/{sub-05_ses-007_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-05_ses-007_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-05/ses-007/fmap/{sub-05_ses-007_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-05_ses-007_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-05/ses-007/fmap/{sub-05_ses-007_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-05_ses-007_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-05/ses-007/fmap/{sub-05_ses-007_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-05_ses-007_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz rename sub-05/ses-007/fmap/{sub-05_ses-007_acq-sbref_dir-PA_run-06_part-mag_epi.json => sub-05_ses-007_acq-sbref_dir-PA_run-06_epi.json} (100%) rename sub-05/ses-007/fmap/{sub-05_ses-007_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz => sub-05_ses-007_acq-sbref_dir-PA_run-06_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_part-phase_epi.json delete mode 120000 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz rename sub-05/ses-007/fmap/{sub-05_ses-007_acq-sbref_dir-PA_run-07_part-mag_epi.json => sub-05_ses-007_acq-sbref_dir-PA_run-07_epi.json} (100%) rename sub-05/ses-007/fmap/{sub-05_ses-007_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz => sub-05_ses-007_acq-sbref_dir-PA_run-07_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_part-phase_epi.json delete mode 120000 sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 87449327e..000000000 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:51:24.185000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": 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"ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0389973, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [581, -7286, -8780, 451, 0, -324, -29, 101], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 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"StudyID": "1", - "StudyTime": "184920.749000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["185124.185000", "185125.675000", "185127.165000"], - "ContentTime": ["185209.978000", "185209.981000", "185209.983000"], - "InstanceCreationTime": ["185209.978000", "185209.981000", "185209.983000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4804.0, 4806.0, 4826.0], - "WindowWidth": [18544.0, 18548.0, 18574.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 93f4492a3..000000000 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/4V/P9/MD5E-s3334265--f38fa2249407f4e6d421765545e254bc.nii.gz/MD5E-s3334265--f38fa2249407f4e6d421765545e254bc.nii.gz \ No newline at end of file diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 951572ec3..000000000 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:51:13.755000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999758, - -0.0113229, - 0.0188841, - 0.0176254, - 0.925581, - -0.37814 - ], - "ImageOrientationText": "Tra>Cor(-22.2)>Sag(0.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0389973, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 581, - -7286, - -8780, - 451, - 0, - -324, - -29, - 101 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 252.799, - "WipMemBlock": "ea6fe19d-5f3d-48c9-a0df-d512e43eedad||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 73e2133af..000000000 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/wW/GZ/MD5E-s1112192--4128aedcf5f402cea298c7ad19e33de1.nii.gz/MD5E-s1112192--4128aedcf5f402cea298c7ad19e33de1.nii.gz \ No newline at end of file diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index e14acff87..000000000 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:52:43.585000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999758, - -0.0113229, - 0.0188841, - 0.0176254, - 0.925581, - -0.37814 - ], - "ImageOrientationText": "Tra>Cor(-22.2)>Sag(0.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - 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"SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 581, - -7286, - -8780, - 451, - 0, - -324, - -29, - 101 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 252.799, - "WipMemBlock": "cca990a6-6ad6-49c1-badd-f64533e4bc5d||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 6d8c3946c..000000000 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/5F/jP/MD5E-s1103543--c7be9800451d4270b381bf8ddefe46dc.nii.gz/MD5E-s1103543--c7be9800451d4270b381bf8ddefe46dc.nii.gz \ No newline at end of file diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index b2b218a14..000000000 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:02:55.732500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of 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b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 457ef208e..000000000 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Vj/k1/MD5E-s1103523--c429acd36b535bd3b284a421f8dbf56a.nii.gz/MD5E-s1103523--c429acd36b535bd3b284a421f8dbf56a.nii.gz \ No newline at end of file diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index fe67f38db..000000000 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:11:26.487500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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-../../../.git/annex/objects/JF/jF/MD5E-s1103697--3dd2011ee434d429f43ca033047ca6e1.nii.gz/MD5E-s1103697--3dd2011ee434d429f43ca033047ca6e1.nii.gz \ No newline at end of file diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 08afc20c5..000000000 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:21:17.957500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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"%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0488992, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 581, - -7286, - -8780, - 451, - 0, - -324, - -29, - 101 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 252.799, - "WipMemBlock": "a21a22c2-b05f-4d6d-b528-aed23bc8125b||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 34b46fcf2..000000000 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/74/mx/MD5E-s1103649--f7cd518ddf0932b8163aa14ad6c5f8ab.nii.gz/MD5E-s1103649--f7cd518ddf0932b8163aa14ad6c5f8ab.nii.gz \ No newline at end of file diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index 32859a824..000000000 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:34:1.570000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999758, - -0.0113229, - 0.0188841, - 0.0176254, - 0.925581, - -0.37814 - ], - "ImageOrientationText": "Tra>Cor(-22.2)>Sag(0.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - 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"SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 581, - -7286, - -8780, - 451, - 0, - -324, - -29, - 101 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 252.799, - "WipMemBlock": "09a24fc3-4c5a-4b82-9357-f4feb7b90136||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index 761702214..000000000 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/2M/VM/MD5E-s1103529--2d8034efe944d9a6770201b2f4e1917d.nii.gz/MD5E-s1103529--2d8034efe944d9a6770201b2f4e1917d.nii.gz \ No newline at end of file diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_part-mag_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_epi.json similarity index 100% rename from sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_part-mag_epi.json rename to sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_epi.json diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_epi.nii.gz similarity index 100% rename from sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz rename to sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_epi.nii.gz diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_part-phase_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_part-phase_epi.json deleted file mode 100644 index 36976130e..000000000 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:42:47.617500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999758, - -0.0113229, - 0.0188841, - 0.0176254, - 0.925581, - -0.37814 - ], - "ImageOrientationText": "Tra>Cor(-22.2)>Sag(0.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-06", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0488992, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-06_SBRef", - "SeriesNumber": 24, - "ShimSetting": [ - 581, - -7286, - -8780, - 451, - 0, - -324, - -29, - 101 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 252.799, - "WipMemBlock": "f4764476-e471-4926-b173-6891b1079903||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz deleted file mode 120000 index 8b5893d85..000000000 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Vf/z0/MD5E-s1103866--62e32401bcc3920c5cbd6b6437c2a044.nii.gz/MD5E-s1103866--62e32401bcc3920c5cbd6b6437c2a044.nii.gz \ No newline at end of file diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_part-mag_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_epi.json similarity index 100% rename from sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_part-mag_epi.json rename to sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_epi.json diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_epi.nii.gz similarity index 100% rename from sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz rename to sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_epi.nii.gz diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_part-phase_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_part-phase_epi.json deleted file mode 100644 index 17a06ad3d..000000000 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:51:38.747500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999758, - -0.0113229, - 0.0188841, - 0.0176254, - 0.925581, - -0.37814 - ], - "ImageOrientationText": "Tra>Cor(-22.2)>Sag(0.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-07", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0488992, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-07_SBRef", - "SeriesNumber": 27, - "ShimSetting": [ - 581, - -7286, - -8780, - 451, - 0, - -324, - -29, - 101 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 252.799, - "WipMemBlock": "60772268-e493-449e-9034-e6ba0f5c5d3a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz deleted file mode 120000 index 30c2dedfc..000000000 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/mj/Xj/MD5E-s1103567--ea8518c9cb11e4674e4854b7d13382db.nii.gz/MD5E-s1103567--ea8518c9cb11e4674e4854b7d13382db.nii.gz \ No newline at end of file diff --git a/sub-05/ses-007/sub-05_ses-007_scans.tsv b/sub-05/ses-007/sub-05_ses-007_scans.tsv index b46a892e8..c5ca118bd 120000 --- a/sub-05/ses-007/sub-05_ses-007_scans.tsv +++ b/sub-05/ses-007/sub-05_ses-007_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/q5/7m/MD5E-s5155--3528bfe6849c7908205d5e13358825b8.tsv/MD5E-s5155--3528bfe6849c7908205d5e13358825b8.tsv \ No newline at end of file +../../.git/annex/objects/2W/mZ/MD5E-s4070--227c070a668f68d28d4f6bca5eb00e61.tsv/MD5E-s4070--227c070a668f68d28d4f6bca5eb00e61.tsv \ No newline at end of file From 1c200cf5f688d95c1d985742e6ccd18438cd89b3 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:44:35 -0400 Subject: [PATCH 370/463] fix complex event files --- ...g_events.tsv => sub-05_ses-006_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-05_ses-006_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-05_ses-006_task-mario3_run-03_events.tsv} | 0 ...e_events.tsv => sub-05_ses-006_task-mario3_run-04_events.tsv} | 0 .../func/sub-05_ses-006_task-mario3_run-04_part-phase_events.tsv | 1 - ...g_events.tsv => sub-05_ses-006_task-mario3_run-05_events.tsv} | 0 .../func/sub-05_ses-006_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-05_ses-006_task-mario3_run-05_part-phase_events.tsv | 1 - ...e_events.tsv => sub-05_ses-006_task-mario3_run-06_events.tsv} | 0 .../func/sub-05_ses-006_task-mario3_run-06_part-mag_events.tsv | 1 - .../func/sub-05_ses-006_task-mario3_run-06_part-phase_events.tsv | 1 - ...g_events.tsv => sub-05_ses-006_task-mario3_run-07_events.tsv} | 0 .../func/sub-05_ses-006_task-mario3_run-07_part-mag_events.tsv | 1 - .../func/sub-05_ses-006_task-mario3_run-07_part-phase_events.tsv | 1 - 14 files changed, 7 deletions(-) rename sub-05/ses-006/func/{sub-05_ses-006_task-mario3_run-01_part-mag_events.tsv => sub-05_ses-006_task-mario3_run-01_events.tsv} (100%) rename sub-05/ses-006/func/{sub-05_ses-006_task-mario3_run-01_part-phase_events.tsv => sub-05_ses-006_task-mario3_run-02_events.tsv} (100%) rename sub-05/ses-006/func/{sub-05_ses-006_task-mario3_run-02_part-mag_events.tsv => sub-05_ses-006_task-mario3_run-03_events.tsv} (100%) rename sub-05/ses-006/func/{sub-05_ses-006_task-mario3_run-02_part-phase_events.tsv => sub-05_ses-006_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-04_part-phase_events.tsv rename sub-05/ses-006/func/{sub-05_ses-006_task-mario3_run-03_part-mag_events.tsv => sub-05_ses-006_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-05_part-phase_events.tsv rename sub-05/ses-006/func/{sub-05_ses-006_task-mario3_run-03_part-phase_events.tsv => sub-05_ses-006_task-mario3_run-06_events.tsv} (100%) delete mode 120000 sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-06_part-mag_events.tsv delete mode 120000 sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-06_part-phase_events.tsv rename sub-05/ses-006/func/{sub-05_ses-006_task-mario3_run-04_part-mag_events.tsv => sub-05_ses-006_task-mario3_run-07_events.tsv} (100%) delete mode 120000 sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-07_part-mag_events.tsv delete mode 120000 sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-07_part-phase_events.tsv diff --git a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-01_part-mag_events.tsv b/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-01_events.tsv similarity index 100% rename from sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-01_part-mag_events.tsv rename to sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-01_events.tsv diff --git a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-01_part-phase_events.tsv b/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-02_events.tsv similarity index 100% rename from sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-01_part-phase_events.tsv rename to sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-02_events.tsv diff --git a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-02_part-mag_events.tsv b/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-03_events.tsv similarity index 100% rename from sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-02_part-mag_events.tsv rename to sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-03_events.tsv diff --git a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-02_part-phase_events.tsv b/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-04_events.tsv similarity index 100% rename from sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-02_part-phase_events.tsv rename to sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-04_events.tsv diff --git a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-04_part-phase_events.tsv b/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-03_part-mag_events.tsv b/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-05_events.tsv similarity index 100% rename from sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-03_part-mag_events.tsv rename to sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-05_events.tsv diff --git a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-05_part-mag_events.tsv b/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-05_part-phase_events.tsv b/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-03_part-phase_events.tsv b/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-06_events.tsv similarity index 100% rename from sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-03_part-phase_events.tsv rename to sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-06_events.tsv diff --git a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-06_part-mag_events.tsv b/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-06_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-06_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-06_part-phase_events.tsv b/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-06_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-06_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-04_part-mag_events.tsv b/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-07_events.tsv similarity index 100% rename from sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-04_part-mag_events.tsv rename to sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-07_events.tsv diff --git a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-07_part-mag_events.tsv b/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-07_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-07_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-07_part-phase_events.tsv b/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-07_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-07_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From fe24fa7054d3441e2af79dc2baf9c758622cde5a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:44:35 -0400 Subject: [PATCH 371/463] fix complex event files --- ...g_events.tsv => sub-05_ses-003_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-05_ses-003_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-05_ses-003_task-mario3_run-03_events.tsv} | 0 ...e_events.tsv => sub-05_ses-003_task-mario3_run-04_events.tsv} | 0 ...g_events.tsv => sub-05_ses-003_task-mario3_run-05_events.tsv} | 0 .../func/sub-05_ses-003_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-05_ses-003_task-mario3_run-05_part-phase_events.tsv | 1 - ...e_events.tsv => sub-05_ses-003_task-mario3_run-06_events.tsv} | 0 .../func/sub-05_ses-003_task-mario3_run-06_part-mag_events.tsv | 1 - .../func/sub-05_ses-003_task-mario3_run-06_part-phase_events.tsv | 1 - ...g_events.tsv => sub-05_ses-003_task-mario3_run-07_events.tsv} | 0 .../func/sub-05_ses-003_task-mario3_run-07_part-mag_events.tsv | 1 - .../func/sub-05_ses-003_task-mario3_run-07_part-phase_events.tsv | 1 - ...e_events.tsv => sub-05_ses-003_task-mario3_run-08_events.tsv} | 0 .../func/sub-05_ses-003_task-mario3_run-08_part-mag_events.tsv | 1 - .../func/sub-05_ses-003_task-mario3_run-08_part-phase_events.tsv | 1 - 16 files changed, 8 deletions(-) rename sub-05/ses-003/func/{sub-05_ses-003_task-mario3_run-01_part-mag_events.tsv => sub-05_ses-003_task-mario3_run-01_events.tsv} (100%) rename sub-05/ses-003/func/{sub-05_ses-003_task-mario3_run-01_part-phase_events.tsv => sub-05_ses-003_task-mario3_run-02_events.tsv} (100%) rename sub-05/ses-003/func/{sub-05_ses-003_task-mario3_run-02_part-mag_events.tsv => sub-05_ses-003_task-mario3_run-03_events.tsv} (100%) rename sub-05/ses-003/func/{sub-05_ses-003_task-mario3_run-02_part-phase_events.tsv => sub-05_ses-003_task-mario3_run-04_events.tsv} (100%) rename sub-05/ses-003/func/{sub-05_ses-003_task-mario3_run-03_part-mag_events.tsv => sub-05_ses-003_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-05_part-phase_events.tsv rename sub-05/ses-003/func/{sub-05_ses-003_task-mario3_run-03_part-phase_events.tsv => sub-05_ses-003_task-mario3_run-06_events.tsv} (100%) delete mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-06_part-mag_events.tsv delete mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-06_part-phase_events.tsv rename sub-05/ses-003/func/{sub-05_ses-003_task-mario3_run-04_part-mag_events.tsv => sub-05_ses-003_task-mario3_run-07_events.tsv} (100%) delete mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-07_part-mag_events.tsv delete mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-07_part-phase_events.tsv rename sub-05/ses-003/func/{sub-05_ses-003_task-mario3_run-04_part-phase_events.tsv => sub-05_ses-003_task-mario3_run-08_events.tsv} (100%) delete mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-08_part-mag_events.tsv delete mode 120000 sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-08_part-phase_events.tsv diff --git a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-01_part-mag_events.tsv b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-01_events.tsv similarity index 100% rename from sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-01_part-mag_events.tsv rename to sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-01_events.tsv diff --git a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-01_part-phase_events.tsv b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_events.tsv similarity index 100% rename from sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-01_part-phase_events.tsv rename to sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_events.tsv diff --git a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_part-mag_events.tsv b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-03_events.tsv similarity index 100% rename from sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_part-mag_events.tsv rename to sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-03_events.tsv diff --git a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_part-phase_events.tsv b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-04_events.tsv similarity index 100% rename from sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_part-phase_events.tsv rename to sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-04_events.tsv diff --git a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-03_part-mag_events.tsv b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-05_events.tsv similarity index 100% rename from sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-03_part-mag_events.tsv rename to sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-05_events.tsv diff --git a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-05_part-mag_events.tsv b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-05_part-phase_events.tsv b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-03_part-phase_events.tsv b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-06_events.tsv similarity index 100% rename from sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-03_part-phase_events.tsv rename to sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-06_events.tsv diff --git a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-06_part-mag_events.tsv b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-06_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-06_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-06_part-phase_events.tsv b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-06_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-06_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-04_part-mag_events.tsv b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-07_events.tsv similarity index 100% rename from sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-04_part-mag_events.tsv rename to sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-07_events.tsv diff --git a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-07_part-mag_events.tsv b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-07_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-07_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-07_part-phase_events.tsv b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-07_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-07_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-04_part-phase_events.tsv b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-08_events.tsv similarity index 100% rename from sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-04_part-phase_events.tsv rename to sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-08_events.tsv diff --git a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-08_part-mag_events.tsv b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-08_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-08_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-08_part-phase_events.tsv b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-08_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-08_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 8a2d99fb85324bef047671493a4c1f9533c5e1d7 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:44:38 -0400 Subject: [PATCH 372/463] fix complex event files --- ...g_events.tsv => sub-05_ses-007_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-05_ses-007_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-05_ses-007_task-mario3_run-03_events.tsv} | 0 ...e_events.tsv => sub-05_ses-007_task-mario3_run-04_events.tsv} | 0 .../func/sub-05_ses-007_task-mario3_run-04_part-phase_events.tsv | 1 - ...g_events.tsv => sub-05_ses-007_task-mario3_run-05_events.tsv} | 0 .../func/sub-05_ses-007_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-05_ses-007_task-mario3_run-05_part-phase_events.tsv | 1 - ...e_events.tsv => sub-05_ses-007_task-mario3_run-06_events.tsv} | 0 .../func/sub-05_ses-007_task-mario3_run-06_part-mag_events.tsv | 1 - .../func/sub-05_ses-007_task-mario3_run-06_part-phase_events.tsv | 1 - ...g_events.tsv => sub-05_ses-007_task-mario3_run-07_events.tsv} | 0 .../func/sub-05_ses-007_task-mario3_run-07_part-mag_events.tsv | 1 - .../func/sub-05_ses-007_task-mario3_run-07_part-phase_events.tsv | 1 - 14 files changed, 7 deletions(-) rename sub-05/ses-007/func/{sub-05_ses-007_task-mario3_run-01_part-mag_events.tsv => sub-05_ses-007_task-mario3_run-01_events.tsv} (100%) rename sub-05/ses-007/func/{sub-05_ses-007_task-mario3_run-01_part-phase_events.tsv => sub-05_ses-007_task-mario3_run-02_events.tsv} (100%) rename sub-05/ses-007/func/{sub-05_ses-007_task-mario3_run-02_part-mag_events.tsv => sub-05_ses-007_task-mario3_run-03_events.tsv} (100%) rename sub-05/ses-007/func/{sub-05_ses-007_task-mario3_run-02_part-phase_events.tsv => sub-05_ses-007_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-04_part-phase_events.tsv rename sub-05/ses-007/func/{sub-05_ses-007_task-mario3_run-03_part-mag_events.tsv => sub-05_ses-007_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-05_part-phase_events.tsv rename sub-05/ses-007/func/{sub-05_ses-007_task-mario3_run-03_part-phase_events.tsv => sub-05_ses-007_task-mario3_run-06_events.tsv} (100%) delete mode 120000 sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-06_part-mag_events.tsv delete mode 120000 sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-06_part-phase_events.tsv rename sub-05/ses-007/func/{sub-05_ses-007_task-mario3_run-04_part-mag_events.tsv => sub-05_ses-007_task-mario3_run-07_events.tsv} (100%) delete mode 120000 sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-07_part-mag_events.tsv delete mode 120000 sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-07_part-phase_events.tsv diff --git a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-01_part-mag_events.tsv b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-01_events.tsv similarity index 100% rename from sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-01_part-mag_events.tsv rename to sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-01_events.tsv diff --git a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-01_part-phase_events.tsv b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-02_events.tsv similarity index 100% rename from sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-01_part-phase_events.tsv rename to sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-02_events.tsv diff --git a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-02_part-mag_events.tsv b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-03_events.tsv similarity index 100% rename from sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-02_part-mag_events.tsv rename to sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-03_events.tsv diff --git a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-02_part-phase_events.tsv b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-04_events.tsv similarity index 100% rename from sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-02_part-phase_events.tsv rename to sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-04_events.tsv diff --git a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-04_part-phase_events.tsv b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-03_part-mag_events.tsv b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-05_events.tsv similarity index 100% rename from sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-03_part-mag_events.tsv rename to sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-05_events.tsv diff --git a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-05_part-mag_events.tsv b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-05_part-phase_events.tsv b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-03_part-phase_events.tsv b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-06_events.tsv similarity index 100% rename from sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-03_part-phase_events.tsv rename to sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-06_events.tsv diff --git a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-06_part-mag_events.tsv b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-06_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-06_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-06_part-phase_events.tsv b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-06_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-06_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-04_part-mag_events.tsv b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-07_events.tsv similarity index 100% rename from sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-04_part-mag_events.tsv rename to sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-07_events.tsv diff --git a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-07_part-mag_events.tsv b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-07_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-07_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-07_part-phase_events.tsv b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-07_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-07_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 12c3adb3c8c60ba3fe878a2ad106b2fce13455bb Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:44:56 -0400 Subject: [PATCH 373/463] fill IntendedFor --- ...5_ses-006_acq-sbref_dir-AP_run-01_epi.json | 94 +++---------------- ...5_ses-006_acq-sbref_dir-PA_run-01_epi.json | 88 ++--------------- ...5_ses-006_acq-sbref_dir-PA_run-02_epi.json | 88 ++--------------- ...5_ses-006_acq-sbref_dir-PA_run-03_epi.json | 88 ++--------------- ...5_ses-006_acq-sbref_dir-PA_run-04_epi.json | 88 ++--------------- ...5_ses-006_acq-sbref_dir-PA_run-05_epi.json | 88 ++--------------- ...5_ses-006_acq-sbref_dir-PA_run-06_epi.json | 88 ++--------------- ...5_ses-006_acq-sbref_dir-PA_run-07_epi.json | 88 ++--------------- 8 files changed, 62 insertions(+), 648 deletions(-) diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_epi.json index d7afff205..7b0e7006e 100644 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999757, - 0.00248157, - 0.021882, - 0.00610732, - 0.923415, - -0.383756 - ], + "ImageOrientationPatientDICOM": [0.999757, 0.00248157, 0.021882, 0.00610732, 0.923415, -0.383756], "ImageOrientationText": "Tra>Cor(-22.6)>Sag(1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,21 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-05_ses-006_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-006/func/sub-05_ses-006_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-006/func/sub-05_ses-006_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-006/func/sub-05_ses-006_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-006/func/sub-05_ses-006_task-mario3_run-05_part-mag_bold.nii.gz", + "ses-006/func/sub-05_ses-006_task-mario3_run-06_part-mag_bold.nii.gz", + "ses-006/func/sub-05_ses-006_task-mario3_run-07_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +69,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 587, - -7295, - -8810, - 404, - 24, - -362, - -45, - 96 - ], + "ShimSetting": [587, -7295, -8810, 404, 24, -362, -45, 96], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_epi.json index fd9fa8494..88a6d31c5 100644 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999757, - 0.00248157, - 0.021882, - 0.00610732, - 0.923415, - -0.383756 - ], + "ImageOrientationPatientDICOM": [0.999757, 0.00248157, 0.021882, 0.00610732, 0.923415, -0.383756], "ImageOrientationText": "Tra>Cor(-22.6)>Sag(1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-05_ses-006_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 587, - -7295, - -8810, - 404, - 24, - -363, - -45, - 95 - ], + "ShimSetting": [587, -7295, -8810, 404, 24, -363, -45, 95], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_epi.json index f9c202dd2..90b408d67 100644 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999757, - 0.00248157, - 0.021882, - 0.00610732, - 0.923415, - -0.383756 - ], + "ImageOrientationPatientDICOM": [0.999757, 0.00248157, 0.021882, 0.00610732, 0.923415, -0.383756], "ImageOrientationText": "Tra>Cor(-22.6)>Sag(1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-05_ses-006_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 587, - -7295, - -8810, - 404, - 24, - -363, - -45, - 95 - ], + "ShimSetting": [587, -7295, -8810, 404, 24, -363, -45, 95], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_epi.json index 288b8208d..7deb84b29 100644 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999757, - 0.00248157, - 0.021882, - 0.00610732, - 0.923415, - -0.383756 - ], + "ImageOrientationPatientDICOM": [0.999757, 0.00248157, 0.021882, 0.00610732, 0.923415, -0.383756], "ImageOrientationText": "Tra>Cor(-22.6)>Sag(1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-05_ses-006_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 587, - -7295, - -8810, - 404, - 24, - -363, - -45, - 95 - ], + "ShimSetting": [587, -7295, -8810, 404, 24, -363, -45, 95], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_epi.json index 3cdaa27fb..5250a54ce 100644 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999757, - 0.00248157, - 0.021882, - 0.00610732, - 0.923415, - -0.383756 - ], + "ImageOrientationPatientDICOM": [0.999757, 0.00248157, 0.021882, 0.00610732, 0.923415, -0.383756], "ImageOrientationText": "Tra>Cor(-22.6)>Sag(1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-05_ses-006_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 587, - -7295, - -8810, - 404, - 24, - -363, - -45, - 95 - ], + "ShimSetting": [587, -7295, -8810, 404, 24, -363, -45, 95], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_epi.json index b4ac01c5e..52b964155 100644 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999757, - 0.00248157, - 0.021882, - 0.00610732, - 0.923415, - -0.383756 - ], + "ImageOrientationPatientDICOM": [0.999757, 0.00248157, 0.021882, 0.00610732, 0.923415, -0.383756], "ImageOrientationText": "Tra>Cor(-22.6)>Sag(1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-05_ses-006_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 587, - -7295, - -8810, - 404, - 24, - -363, - -45, - 95 - ], + "ShimSetting": [587, -7295, -8810, 404, 24, -363, -45, 95], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_epi.json index d03edb443..89e4e3ba9 100644 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_epi.json +++ b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-06_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999757, - 0.00248157, - 0.021882, - 0.00610732, - 0.923415, - -0.383756 - ], + "ImageOrientationPatientDICOM": [0.999757, 0.00248157, 0.021882, 0.00610732, 0.923415, -0.383756], "ImageOrientationText": "Tra>Cor(-22.6)>Sag(1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-05_ses-006_task-mario3_run-06_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-06_SBRef", "SeriesNumber": 24, - "ShimSetting": [ - 587, - -7295, - -8810, - 404, - 24, - -363, - -45, - 95 - ], + "ShimSetting": [587, -7295, -8810, 404, 24, -363, -45, 95], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_epi.json b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_epi.json index 4ba7b5f12..fa7854e7b 100644 --- a/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_epi.json +++ b/sub-05/ses-006/fmap/sub-05_ses-006_acq-sbref_dir-PA_run-07_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999757, - 0.00248157, - 0.021882, - 0.00610732, - 0.923415, - -0.383756 - ], + "ImageOrientationPatientDICOM": [0.999757, 0.00248157, 0.021882, 0.00610732, 0.923415, -0.383756], "ImageOrientationText": "Tra>Cor(-22.6)>Sag(1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-05_ses-006_task-mario3_run-07_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-07_SBRef", "SeriesNumber": 27, - "ShimSetting": [ - 587, - -7295, - -8810, - 404, - 24, - -363, - -45, - 95 - ], + "ShimSetting": [587, -7295, -8810, 404, 24, -363, -45, 95], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From eb01fa66533b622377d17d08f10a520abb987a2a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:44:57 -0400 Subject: [PATCH 374/463] fill IntendedFor --- ...5_ses-003_acq-sbref_dir-AP_run-01_epi.json | 95 +++---------------- ...5_ses-003_acq-sbref_dir-PA_run-01_epi.json | 88 ++--------------- ...5_ses-003_acq-sbref_dir-PA_run-02_epi.json | 88 ++--------------- ...5_ses-003_acq-sbref_dir-PA_run-03_epi.json | 88 ++--------------- ...5_ses-003_acq-sbref_dir-PA_run-04_epi.json | 88 ++--------------- ...5_ses-003_acq-sbref_dir-PA_run-05_epi.json | 88 ++--------------- ...5_ses-003_acq-sbref_dir-PA_run-06_epi.json | 88 ++--------------- ...5_ses-003_acq-sbref_dir-PA_run-07_epi.json | 88 ++--------------- ...5_ses-003_acq-sbref_dir-PA_run-08_epi.json | 88 ++--------------- 9 files changed, 70 insertions(+), 729 deletions(-) diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_epi.json index a22bf039a..48b16d774 100644 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0144349, - 0.00811844, - 0.0164053, - 0.930407, - -0.366161 - ], + "ImageOrientationPatientDICOM": [0.999863, -0.0144349, 0.00811844, 0.0164053, 0.930407, -0.366161], "ImageOrientationText": "Tra>Cor(-21.5)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,22 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-05_ses-003_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-003/func/sub-05_ses-003_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-003/func/sub-05_ses-003_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-003/func/sub-05_ses-003_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-003/func/sub-05_ses-003_task-mario3_run-05_part-mag_bold.nii.gz", + "ses-003/func/sub-05_ses-003_task-mario3_run-06_part-mag_bold.nii.gz", + "ses-003/func/sub-05_ses-003_task-mario3_run-07_part-mag_bold.nii.gz", + "ses-003/func/sub-05_ses-003_task-mario3_run-08_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +70,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 599, - -7261, - -8811, - 450, - 13, - -363, - -8, - 32 - ], + "ShimSetting": [599, -7261, -8811, 450, 13, -363, -8, 32], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_epi.json index 7ae72a7d7..19ae56402 100644 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0144349, - 0.00811844, - 0.0164053, - 0.930407, - -0.366161 - ], + "ImageOrientationPatientDICOM": [0.999863, -0.0144349, 0.00811844, 0.0164053, 0.930407, -0.366161], "ImageOrientationText": "Tra>Cor(-21.5)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-05_ses-003_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 599, - -7261, - -8811, - 450, - 13, - -363, - -8, - 32 - ], + "ShimSetting": [599, -7261, -8811, 450, 13, -363, -8, 32], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_epi.json index 69d3f60d3..889690204 100644 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0144349, - 0.00811844, - 0.0164053, - 0.930407, - -0.366161 - ], + "ImageOrientationPatientDICOM": [0.999863, -0.0144349, 0.00811844, 0.0164053, 0.930407, -0.366161], "ImageOrientationText": "Tra>Cor(-21.5)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-05_ses-003_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 599, - -7261, - -8811, - 450, - 13, - -363, - -8, - 32 - ], + "ShimSetting": [599, -7261, -8811, 450, 13, -363, -8, 32], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_epi.json index cf30874cc..aeaeb1b9a 100644 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0144349, - 0.00811844, - 0.0164053, - 0.930407, - -0.366161 - ], + "ImageOrientationPatientDICOM": [0.999863, -0.0144349, 0.00811844, 0.0164053, 0.930407, -0.366161], "ImageOrientationText": "Tra>Cor(-21.5)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-05_ses-003_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 599, - -7261, - -8811, - 450, - 13, - -363, - -8, - 32 - ], + "ShimSetting": [599, -7261, -8811, 450, 13, -363, -8, 32], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_epi.json index e09e6247e..b5f1ff219 100644 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0144349, - 0.00811844, - 0.0164053, - 0.930407, - -0.366161 - ], + "ImageOrientationPatientDICOM": [0.999863, -0.0144349, 0.00811844, 0.0164053, 0.930407, -0.366161], "ImageOrientationText": "Tra>Cor(-21.5)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-05_ses-003_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 599, - -7261, - -8811, - 450, - 13, - -363, - -8, - 32 - ], + "ShimSetting": [599, -7261, -8811, 450, 13, -363, -8, 32], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_epi.json index 83d88688a..96d25d56c 100644 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0144349, - 0.00811844, - 0.0164053, - 0.930407, - -0.366161 - ], + "ImageOrientationPatientDICOM": [0.999863, -0.0144349, 0.00811844, 0.0164053, 0.930407, -0.366161], "ImageOrientationText": "Tra>Cor(-21.5)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-05_ses-003_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 599, - -7261, - -8811, - 450, - 13, - -363, - -8, - 32 - ], + "ShimSetting": [599, -7261, -8811, 450, 13, -363, -8, 32], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_epi.json index a1df98cb0..269b06155 100644 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_epi.json +++ b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-06_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0144349, - 0.00811844, - 0.0164053, - 0.930407, - -0.366161 - ], + "ImageOrientationPatientDICOM": [0.999863, -0.0144349, 0.00811844, 0.0164053, 0.930407, -0.366161], "ImageOrientationText": "Tra>Cor(-21.5)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-05_ses-003_task-mario3_run-06_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-06_SBRef", "SeriesNumber": 24, - "ShimSetting": [ - 599, - -7261, - -8811, - 450, - 13, - -363, - -8, - 32 - ], + "ShimSetting": [599, -7261, -8811, 450, 13, -363, -8, 32], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_epi.json index 429c4fc09..e719a3491 100644 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_epi.json +++ b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-07_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0144349, - 0.00811844, - 0.0164053, - 0.930407, - -0.366161 - ], + "ImageOrientationPatientDICOM": [0.999863, -0.0144349, 0.00811844, 0.0164053, 0.930407, -0.366161], "ImageOrientationText": "Tra>Cor(-21.5)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-05_ses-003_task-mario3_run-07_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-07_SBRef", "SeriesNumber": 27, - "ShimSetting": [ - 599, - -7261, - -8811, - 450, - 13, - -363, - -8, - 32 - ], + "ShimSetting": [599, -7261, -8811, 450, 13, -363, -8, 32], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_epi.json b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_epi.json index 43a626784..3527344f6 100644 --- a/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_epi.json +++ b/sub-05/ses-003/fmap/sub-05_ses-003_acq-sbref_dir-PA_run-08_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999863, - -0.0144349, - 0.00811844, - 0.0164053, - 0.930407, - -0.366161 - ], + "ImageOrientationPatientDICOM": [0.999863, -0.0144349, 0.00811844, 0.0164053, 0.930407, -0.366161], "ImageOrientationText": "Tra>Cor(-21.5)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-003/func/sub-05_ses-003_task-mario3_run-08_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-08_SBRef", "SeriesNumber": 30, - "ShimSetting": [ - 599, - -7261, - -8811, - 450, - 13, - -363, - -8, - 32 - ], + "ShimSetting": [599, -7261, -8811, 450, 13, -363, -8, 32], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 4e3ca8bb3d2725e7ed8c70277b4b424b53222e15 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:45:01 -0400 Subject: [PATCH 375/463] fill IntendedFor --- ...5_ses-007_acq-sbref_dir-AP_run-01_epi.json | 94 +++---------------- ...5_ses-007_acq-sbref_dir-PA_run-01_epi.json | 88 ++--------------- ...5_ses-007_acq-sbref_dir-PA_run-02_epi.json | 88 ++--------------- ...5_ses-007_acq-sbref_dir-PA_run-03_epi.json | 88 ++--------------- ...5_ses-007_acq-sbref_dir-PA_run-04_epi.json | 88 ++--------------- ...5_ses-007_acq-sbref_dir-PA_run-05_epi.json | 88 ++--------------- ...5_ses-007_acq-sbref_dir-PA_run-06_epi.json | 88 ++--------------- ...5_ses-007_acq-sbref_dir-PA_run-07_epi.json | 88 ++--------------- 8 files changed, 62 insertions(+), 648 deletions(-) diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_epi.json index 80fe7f8f3..aaae6c8de 100644 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999758, - -0.0113229, - 0.0188841, - 0.0176254, - 0.925581, - -0.37814 - ], + "ImageOrientationPatientDICOM": [0.999758, -0.0113229, 0.0188841, 0.0176254, 0.925581, -0.37814], "ImageOrientationText": "Tra>Cor(-22.2)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,21 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-05_ses-007_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-007/func/sub-05_ses-007_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-007/func/sub-05_ses-007_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-007/func/sub-05_ses-007_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-007/func/sub-05_ses-007_task-mario3_run-05_part-mag_bold.nii.gz", + "ses-007/func/sub-05_ses-007_task-mario3_run-06_part-mag_bold.nii.gz", + "ses-007/func/sub-05_ses-007_task-mario3_run-07_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +69,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 581, - -7286, - -8780, - 451, - 0, - -324, - -29, - 101 - ], + "ShimSetting": [581, -7286, -8780, 451, 0, -324, -29, 101], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_epi.json index 8b217c675..0c06145c5 100644 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999758, - -0.0113229, - 0.0188841, - 0.0176254, - 0.925581, - -0.37814 - ], + "ImageOrientationPatientDICOM": [0.999758, -0.0113229, 0.0188841, 0.0176254, 0.925581, -0.37814], "ImageOrientationText": "Tra>Cor(-22.2)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-05_ses-007_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 581, - -7286, - -8780, - 451, - 0, - -324, - -29, - 101 - ], + "ShimSetting": [581, -7286, -8780, 451, 0, -324, -29, 101], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_epi.json index 72478cccf..fb3015c2b 100644 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999758, - -0.0113229, - 0.0188841, - 0.0176254, - 0.925581, - -0.37814 - ], + "ImageOrientationPatientDICOM": [0.999758, -0.0113229, 0.0188841, 0.0176254, 0.925581, -0.37814], "ImageOrientationText": "Tra>Cor(-22.2)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-05_ses-007_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 581, - -7286, - -8780, - 451, - 0, - -324, - -29, - 101 - ], + "ShimSetting": [581, -7286, -8780, 451, 0, -324, -29, 101], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-03_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-03_epi.json index 78156734e..5fd3d5643 100644 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999758, - -0.0113229, - 0.0188841, - 0.0176254, - 0.925581, - -0.37814 - ], + "ImageOrientationPatientDICOM": [0.999758, -0.0113229, 0.0188841, 0.0176254, 0.925581, -0.37814], "ImageOrientationText": "Tra>Cor(-22.2)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-05_ses-007_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 581, - -7286, - -8780, - 451, - 0, - -324, - -29, - 101 - ], + "ShimSetting": [581, -7286, -8780, 451, 0, -324, -29, 101], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_epi.json index 6ed2a46a9..aebfdcabd 100644 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999758, - -0.0113229, - 0.0188841, - 0.0176254, - 0.925581, - -0.37814 - ], + "ImageOrientationPatientDICOM": [0.999758, -0.0113229, 0.0188841, 0.0176254, 0.925581, -0.37814], "ImageOrientationText": "Tra>Cor(-22.2)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-05_ses-007_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 581, - -7286, - -8780, - 451, - 0, - -324, - -29, - 101 - ], + "ShimSetting": [581, -7286, -8780, 451, 0, -324, -29, 101], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_epi.json index f414484ce..518b7844b 100644 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999758, - -0.0113229, - 0.0188841, - 0.0176254, - 0.925581, - -0.37814 - ], + "ImageOrientationPatientDICOM": [0.999758, -0.0113229, 0.0188841, 0.0176254, 0.925581, -0.37814], "ImageOrientationText": "Tra>Cor(-22.2)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-05_ses-007_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 581, - -7286, - -8780, - 451, - 0, - -324, - -29, - 101 - ], + "ShimSetting": [581, -7286, -8780, 451, 0, -324, -29, 101], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_epi.json index 61008232e..7833d2946 100644 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_epi.json +++ b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-06_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999758, - -0.0113229, - 0.0188841, - 0.0176254, - 0.925581, - -0.37814 - ], + "ImageOrientationPatientDICOM": [0.999758, -0.0113229, 0.0188841, 0.0176254, 0.925581, -0.37814], "ImageOrientationText": "Tra>Cor(-22.2)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-05_ses-007_task-mario3_run-06_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-06_SBRef", "SeriesNumber": 24, - "ShimSetting": [ - 581, - -7286, - -8780, - 451, - 0, - -324, - -29, - 101 - ], + "ShimSetting": [581, -7286, -8780, 451, 0, -324, -29, 101], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_epi.json b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_epi.json index ffc133499..3a9e7738c 100644 --- a/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_epi.json +++ b/sub-05/ses-007/fmap/sub-05_ses-007_acq-sbref_dir-PA_run-07_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999758, - -0.0113229, - 0.0188841, - 0.0176254, - 0.925581, - -0.37814 - ], + "ImageOrientationPatientDICOM": [0.999758, -0.0113229, 0.0188841, 0.0176254, 0.925581, -0.37814], "ImageOrientationText": "Tra>Cor(-22.2)>Sag(0.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-007/func/sub-05_ses-007_task-mario3_run-07_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-07_SBRef", "SeriesNumber": 27, - "ShimSetting": [ - 581, - -7286, - -8780, - 451, - 0, - -324, - -29, - 101 - ], + "ShimSetting": [581, -7286, -8780, 451, 0, -324, -29, 101], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 3d4f33ea5e30726ade18010177839fe078b00cf5 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:54:38 -0400 Subject: [PATCH 376/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..11dec9094 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 31a8cb96-8217-4d23-b84d-27e793e2605b diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..4beaac7e1 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 4beaac7e12c5af30e0961af087e068a9d5320b1b From a32fb9202d9bd667525e648e4ee64338995fcb69 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:55:27 -0400 Subject: [PATCH 377/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..3636b5921 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = bce3c722-3427-48eb-a8e2-1643feb0cc94 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..18526d298 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 18526d2989b4e63ac0f3c4716f8bc6cb8bd20118 From fac15de1b4527ca4a6db2ad8ea949c549779ddd2 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:55:57 -0400 Subject: [PATCH 378/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-03_ses-001_acq-axial_localizer.json | 81 +++ .../sub-03_ses-001_acq-axial_localizer.nii.gz | 1 + .../sub-03_ses-001_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-001_acq-coronal_localizer.nii.gz | 1 + ...sub-03_ses-001_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-001_acq-sagittal_localizer.nii.gz | 1 + sub-03/ses-001/anat/sub-03_ses-001_scout.json | 542 ++++++++++++++++++ .../ses-001/anat/sub-03_ses-001_scout.nii.gz | 1 + ...1_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ...-001_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-01_part-mag_events.tsv | 1 + ...001_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-01_part-phase_events.tsv | 1 + ...1_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-001_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-02_part-mag_events.tsv | 1 + ...001_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-02_part-phase_events.tsv | 1 + ...1_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-001_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-03_part-mag_events.tsv | 1 + ...001_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-03_part-phase_events.tsv | 1 + ...1_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-001_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-04_part-mag_events.tsv | 1 + ...001_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-04_part-phase_events.tsv | 1 + ...1_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-001_task-mario3_run-05_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-05_part-mag_events.tsv | 1 + ...001_task-mario3_run-05_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-05_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-05_part-phase_events.tsv | 1 + ...1_task-mario3_run-05_part-phase_sbref.json | 153 +++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + sub-03/ses-001/sub-03_ses-001_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 93 files changed, 6371 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-001/anat/sub-03_ses-001_acq-axial_localizer.json create mode 120000 sub-03/ses-001/anat/sub-03_ses-001_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-001/anat/sub-03_ses-001_acq-coronal_localizer.json create mode 120000 sub-03/ses-001/anat/sub-03_ses-001_acq-coronal_localizer.nii.gz create mode 100644 sub-03/ses-001/anat/sub-03_ses-001_acq-sagittal_localizer.json create mode 120000 sub-03/ses-001/anat/sub-03_ses-001_acq-sagittal_localizer.nii.gz create mode 100644 sub-03/ses-001/anat/sub-03_ses-001_scout.json create mode 120000 sub-03/ses-001/anat/sub-03_ses-001_scout.nii.gz create mode 100644 sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 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160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 4beaac7e12c5af30e0961af087e068a9d5320b1b +Subproject commit 52ca6b55d5e0cf63f4c42efd5e3a602557daeea2 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-03/ses-001/anat/sub-03_ses-001_acq-axial_localizer.json b/sub-03/ses-001/anat/sub-03_ses-001_acq-axial_localizer.json new file mode 100644 index 000000000..f436c85f6 --- /dev/null +++ b/sub-03/ses-001/anat/sub-03_ses-001_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:08:41.045000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + 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b/sub-03/ses-001/anat/sub-03_ses-001_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:08:48.035000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, 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a/sub-03/ses-001/anat/sub-03_ses-001_acq-sagittal_localizer.nii.gz b/sub-03/ses-001/anat/sub-03_ses-001_acq-sagittal_localizer.nii.gz new file mode 120000 index 000000000..9571c6a7a --- /dev/null +++ b/sub-03/ses-001/anat/sub-03_ses-001_acq-sagittal_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/4V/0p/MD5E-s586198--40f8cca3e75753884777734975afaa81.nii.gz/MD5E-s586198--40f8cca3e75753884777734975afaa81.nii.gz \ No newline at end of file diff --git a/sub-03/ses-001/anat/sub-03_ses-001_scout.json b/sub-03/ses-001/anat/sub-03_ses-001_scout.json new file mode 100644 index 000000000..60c997366 --- /dev/null +++ b/sub-03/ses-001/anat/sub-03_ses-001_scout.json @@ -0,0 +1,542 @@ +{ + "AcquisitionMatrixPE": 160, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:08:18.990000", + "BaseResolution": 160, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + 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"TxRefAmp": 251.722, + "dcmmeta_affine": [ + [-1.9994570016860962, -0.008724396117031574, 0.045777060091495514, 108.27404022216797], + [-0.02055763639509678, 1.9282715320587158, -0.5304208397865295, -71.975341796875], + [0.041821498423814774, 0.5307473540306091, 1.9278377294540405, -57.614044189453125], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 5670ba5af53f0aff9270cc47cb3d45b5a92d6fa3 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:56:07 -0400 Subject: [PATCH 379/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-03_ses-019_acq-axial_localizer.json | 81 +++ .../sub-03_ses-019_acq-axial_localizer.nii.gz | 1 + .../sub-03_ses-019_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-019_acq-coronal_localizer.nii.gz | 1 + ...sub-03_ses-019_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-019_acq-sagittal_localizer.nii.gz | 1 + sub-03/ses-019/anat/sub-03_ses-019_scout.json | 542 ++++++++++++++++++ .../ses-019/anat/sub-03_ses-019_scout.nii.gz | 1 + ...9_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ...-019_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...19_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...019_task-mario3_run-01_part-mag_events.tsv | 1 + ...019_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...19_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-01_part-phase_events.tsv | 1 + ...9_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-019_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...19_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...019_task-mario3_run-02_part-mag_events.tsv | 1 + ...019_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...19_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-02_part-phase_events.tsv | 1 + ...9_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-019_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...19_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...019_task-mario3_run-03_part-mag_events.tsv | 1 + ...019_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...19_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-03_part-phase_events.tsv | 1 + ...9_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-019_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...19_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...019_task-mario3_run-04_part-mag_events.tsv | 1 + ...019_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...19_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-04_part-phase_events.tsv | 1 + ...9_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-019_task-mario3_run-05_part-mag_bold.json | 172 ++++++ ...19_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...019_task-mario3_run-05_part-mag_events.tsv | 1 + ...019_task-mario3_run-05_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...19_task-mario3_run-05_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-05_part-phase_events.tsv | 1 + ...9_task-mario3_run-05_part-phase_sbref.json | 153 +++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + sub-03/ses-019/sub-03_ses-019_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 93 files changed, 6371 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-019/anat/sub-03_ses-019_acq-axial_localizer.json create mode 120000 sub-03/ses-019/anat/sub-03_ses-019_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-019/anat/sub-03_ses-019_acq-coronal_localizer.json create mode 120000 sub-03/ses-019/anat/sub-03_ses-019_acq-coronal_localizer.nii.gz create mode 100644 sub-03/ses-019/anat/sub-03_ses-019_acq-sagittal_localizer.json create mode 120000 sub-03/ses-019/anat/sub-03_ses-019_acq-sagittal_localizer.nii.gz create mode 100644 sub-03/ses-019/anat/sub-03_ses-019_scout.json create mode 120000 sub-03/ses-019/anat/sub-03_ses-019_scout.nii.gz create mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_part-mag_epi.json create mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz create mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_part-phase_epi.json create mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-mag_bold.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-mag_bold.nii.gz create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-mag_events.tsv create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-mag_sbref.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-phase_bold.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-phase_bold.nii.gz create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-phase_events.tsv create mode 100644 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-phase_sbref.json create mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-phase_sbref.nii.gz create mode 120000 sub-03/ses-019/sub-03_ses-019_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 18526d298..82d0b6aec 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 18526d2989b4e63ac0f3c4716f8bc6cb8bd20118 +Subproject commit 82d0b6aec78994eb4f64f9660152dce497daa5b9 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-03/ses-019/anat/sub-03_ses-019_acq-axial_localizer.json b/sub-03/ses-019/anat/sub-03_ses-019_acq-axial_localizer.json new file mode 100644 index 000000000..b8c920acf --- /dev/null +++ b/sub-03/ses-019/anat/sub-03_ses-019_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:42:53.007500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + 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"SliceThickness": 2, + "SliceTiming": [ + 0, + 0.1, + 0.1975, + 0.295, + 0.3925, + 0.49, + 0.59, + 0.6875, + 0.785, + 0.8825, + 0.98, + 1.08, + 1.1775, + 1.275, + 1.3725, + 1.47, + 1.57, + 1.6675, + 1.765, + 1.8625, + 1.96, + 2.06, + 2.1575, + 2.255, + 2.3525, + 2.45, + 2.5475, + 2.6475, + 2.745, + 2.8425, + 2.94, + 3.0375, + 3.1375, + 3.235, + 3.3325, + 3.43, + 3.5275, + 3.6275, + 3.725, + 3.8225, + 3.92, + 4.0175, + 4.1175, + 4.215, + 4.3125, + 4.41, + 4.5075, + 4.6075, + 4.705, + 4.8025, + 4.9, + 4.9975, + 5.0975, + 5.195, + 5.2925, + 5.39, + 5.4875, + 5.5875, + 5.685, + 5.7825 + ], + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 233.337, + "WipMemBlock": "fd520a17-1abc-4369-b6e6-2fd0a5f6cbb1||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-phase_sbref.nii.gz b/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-phase_sbref.nii.gz new file mode 120000 index 000000000..7ef4e505e --- /dev/null +++ b/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/fj/Wv/MD5E-s1103669--3f1cdcb2f71f67d3e6e5668fd4fdff4b.nii.gz/MD5E-s1103669--3f1cdcb2f71f67d3e6e5668fd4fdff4b.nii.gz \ No newline at end of file diff --git a/sub-03/ses-019/sub-03_ses-019_scans.tsv b/sub-03/ses-019/sub-03_ses-019_scans.tsv new file mode 120000 index 000000000..be28190f7 --- /dev/null +++ b/sub-03/ses-019/sub-03_ses-019_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/2G/xK/MD5E-s3911--89d0f4ce889847b78b81c5b116e13a69.tsv/MD5E-s3911--89d0f4ce889847b78b81c5b116e13a69.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..dde8a3b7a --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999388, 0.019371, 0.0291166, -0.00994255, 0.955603, -0.294491], + "ImageOrientationText": "Tra>Cor(-17.1)>Sag(1.9)", + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0632438, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [622, -7201, -8762, 694, 63, 15, -20, 5], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 233.337, + "dcmmeta_affine": [ + [-1.9987765550613403, -0.019885102286934853, 0.06705693155527115, 107.79051208496094], + [-0.038742098957300186, 1.9112052917480469, -0.5880419015884399, -69.23804473876953], + [0.058233149349689484, 0.5889811515808105, 1.910421371459961, -61.62661361694336], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From e812017452633fadd6e889c10e0d3ed818a57f6a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:56:52 -0400 Subject: [PATCH 380/463] fix fmap phase --- ...3_ses-001_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-001_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-001_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - sub-03/ses-001/sub-03_ses-001_scans.tsv | 2 +- 29 files changed, 1 insertion(+), 1097 deletions(-) rename sub-03/ses-001/fmap/{sub-03_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-001_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-001/fmap/{sub-03_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-001_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-001/fmap/{sub-03_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-001_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-001/fmap/{sub-03_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-001_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-001/fmap/{sub-03_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-001_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-001/fmap/{sub-03_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-001_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-001/fmap/{sub-03_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-001_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-001/fmap/{sub-03_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-001_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-03/ses-001/fmap/{sub-03_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-03_ses-001_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-03/ses-001/fmap/{sub-03_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-03_ses-001_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-03/ses-001/fmap/{sub-03_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-03_ses-001_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-03/ses-001/fmap/{sub-03_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-03_ses-001_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-03/ses-001/fmap/{sub-03_ses-001_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-03_ses-001_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-03/ses-001/fmap/{sub-03_ses-001_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-03_ses-001_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index a01fb471d..000000000 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:09:45.480000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999729, 0.0102788, 0.0209107, -0.0043622, 0.964136, -0.265374], - "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": 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ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9994570016860962, -0.008724396117031574, 0.045777060091495514, 108.27404022216797], - [-0.02055763639509678, 1.9282715320587158, -0.5304208397865295, -71.975341796875], - [0.041821498423814774, 0.5307473540306091, 1.9278377294540405, -57.614044189453125], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99972850635729, 0.01027881841347, 0.02091075007376, -0.0043621981171, 0.96413576918669, 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[18620.0, 18650.0, 18620.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 86c2a4fa7..000000000 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/gK/kP/MD5E-s3334684--96324ee674ebc14bd7988ca032aac6ec.nii.gz/MD5E-s3334684--96324ee674ebc14bd7988ca032aac6ec.nii.gz \ No newline at end of file diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 51f4b005a..000000000 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:09:35.050000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999729, - 0.0102788, - 0.0209107, - -0.0043622, - 0.964136, - -0.265374 - ], - "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": 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0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.722, - "WipMemBlock": "32eb0bac-7e15-41ea-9140-2e4b7e0ff3da||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index a03d6578d..000000000 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/M3/G7/MD5E-s1112270--1e5cf1b6218cf67e40dd05f49712b052.nii.gz/MD5E-s1112270--1e5cf1b6218cf67e40dd05f49712b052.nii.gz \ No newline at end of file diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 9037e8638..000000000 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:10:38.370000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999729, - 0.0102788, - 0.0209107, - -0.0043622, - 0.964136, - -0.265374 - ], - "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0588891, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 642, - -7213, - -8768, - 706, - 82, - 31, - 47, - -17 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.722, - "WipMemBlock": "75a45855-4327-432d-ab5f-14c47e802c4d||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index b348528dd..000000000 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Z5/xm/MD5E-s1103803--e369d4fedb98c55b6e86377746cf402b.nii.gz/MD5E-s1103803--e369d4fedb98c55b6e86377746cf402b.nii.gz \ No newline at end of file diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index e227d7f54..000000000 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:22:7.407500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.722, - "WipMemBlock": "1777543a-e493-42e4-8b7a-b8a6e0343302||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 244cfafeb..000000000 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/ZW/fz/MD5E-s1103586--15b8c7910a2230e46ba0eae69593d270.nii.gz/MD5E-s1103586--15b8c7910a2230e46ba0eae69593d270.nii.gz \ No newline at end of file diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 6aa3e52fa..000000000 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:30:41.622500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999729, - 0.0102788, - 0.0209107, - -0.0043622, - 0.964136, - -0.265374 - ], - "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0588891, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 642, - -7213, - -8768, - 706, - 82, - 31, - 47, - -17 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.722, - "WipMemBlock": "f975b589-dbe9-4cb0-b79e-fbdbd0b03c45||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index d538e4dd9..000000000 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/z5/0x/MD5E-s1103616--42116f3fd6e3b177f78148dc2e7f62be.nii.gz/MD5E-s1103616--42116f3fd6e3b177f78148dc2e7f62be.nii.gz \ No newline at end of file diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 9909a36d3..000000000 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:40:33.212500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999729, - 0.0102788, - 0.0209107, - -0.0043622, - 0.964136, - -0.265374 - ], - "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0588891, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 642, - -7213, - -8768, - 706, - 82, - 31, - 47, - -17 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.722, - "WipMemBlock": "4da72a08-5918-410c-aad0-92993d9f78bb||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index a7bfdd8fb..000000000 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3Z/jg/MD5E-s1103749--e5a82008e439b3a173492cfd83ff634a.nii.gz/MD5E-s1103749--e5a82008e439b3a173492cfd83ff634a.nii.gz \ No newline at end of file diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index 5631a0114..000000000 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:49:50.372500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999729, - 0.0102788, - 0.0209107, - -0.0043622, - 0.964136, - -0.265374 - ], - "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-05", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0588891, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 642, - -7213, - -8768, - 706, - 82, - 31, - 47, - -17 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.722, - "WipMemBlock": "2c7a6515-0261-4fb7-8a7f-1c1ea8ef4ea3||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index add2bc368..000000000 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/qf/Vq/MD5E-s1103715--7e6d17e51dbd686f7deca6d292f4cea6.nii.gz/MD5E-s1103715--7e6d17e51dbd686f7deca6d292f4cea6.nii.gz \ No newline at end of file diff --git a/sub-03/ses-001/sub-03_ses-001_scans.tsv b/sub-03/ses-001/sub-03_ses-001_scans.tsv index 96d15bff7..8e58f78dc 120000 --- a/sub-03/ses-001/sub-03_ses-001_scans.tsv +++ b/sub-03/ses-001/sub-03_ses-001_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/5K/Mm/MD5E-s3911--39b41b40845f1f20c6095eaed8cc722f.tsv/MD5E-s3911--39b41b40845f1f20c6095eaed8cc722f.tsv \ No newline at end of file +../../.git/annex/objects/ZW/P3/MD5E-s3068--33aaa854c1539a413398b13df116e3c4.tsv/MD5E-s3068--33aaa854c1539a413398b13df116e3c4.tsv \ No newline at end of file From 4b6b2944a5114e8b7ca5d915e63f9a68fce255cb Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:57:03 -0400 Subject: [PATCH 381/463] fix fmap phase --- ...3_ses-019_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-019_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-019_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-019_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-019_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-019_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-019_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-019_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-019_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-019_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-019_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-019_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-019_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-019_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - sub-03/ses-019/sub-03_ses-019_scans.tsv | 2 +- 29 files changed, 1 insertion(+), 1097 deletions(-) rename sub-03/ses-019/fmap/{sub-03_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-019_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-019/fmap/{sub-03_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-019_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-019/fmap/{sub-03_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-019_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-019/fmap/{sub-03_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-019_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-019/fmap/{sub-03_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-019_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-019/fmap/{sub-03_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-019_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-019/fmap/{sub-03_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-019_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-019/fmap/{sub-03_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-019_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-03/ses-019/fmap/{sub-03_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-03_ses-019_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-03/ses-019/fmap/{sub-03_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-03_ses-019_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-03/ses-019/fmap/{sub-03_ses-019_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-03_ses-019_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-03/ses-019/fmap/{sub-03_ses-019_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-03_ses-019_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-03/ses-019/fmap/{sub-03_ses-019_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-03_ses-019_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-03/ses-019/fmap/{sub-03_ses-019_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-03_ses-019_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 03d34e23a..000000000 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:44:3.515000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999388, 0.019371, 0.0291166, -0.00994255, 0.955603, -0.294491], - "ImageOrientationText": 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0.05043720437166, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "154450.030000", - "SliceLocation": -34.894917299429, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999591609, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "152134.849000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["154403.515000", "154405.005000", "154406.495000"], - "ContentTime": ["154450.032000", "154450.034000", "154450.037000"], - "InstanceCreationTime": ["154450.032000", "154450.034000", "154450.037000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4804.0, 4830.0, 4804.0], - "WindowWidth": [18546.0, 18572.0, 18548.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 7f869339d..000000000 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/QX/G5/MD5E-s3334989--1e43807543070345941d6178d0b55034.nii.gz/MD5E-s3334989--1e43807543070345941d6178d0b55034.nii.gz \ No newline at end of file diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index fd62dd0dd..000000000 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:43:53.085000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of 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b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 58b93111a..000000000 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/1m/gJ/MD5E-s1112198--50243d6eb207e850a968d7ed56822e94.nii.gz/MD5E-s1112198--50243d6eb207e850a968d7ed56822e94.nii.gz \ No newline at end of file diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index ab09c6cc8..000000000 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:52:57.562500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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"PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0632438, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 622, - -7201, - -8762, - 694, - 63, - 15, - -20, - 5 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 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-../../../.git/annex/objects/98/Z0/MD5E-s1103743--917a7111a23e04a9807e770c0606eaca.nii.gz/MD5E-s1103743--917a7111a23e04a9807e770c0606eaca.nii.gz \ No newline at end of file diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index ad916e9de..000000000 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:02:58.860000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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- 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 233.337, - "WipMemBlock": "489a4e88-4d1b-4335-89a9-725143fc6a04||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 1868e9233..000000000 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/X1/1W/MD5E-s1103829--bcb6e41033bd9fe4d1a16b585385071e.nii.gz/MD5E-s1103829--bcb6e41033bd9fe4d1a16b585385071e.nii.gz \ No newline at end of file diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 4ea034d8d..000000000 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:13:38.360000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999388, - 0.019371, - 0.0291166, - -0.00994255, - 0.955603, - -0.294491 - ], - "ImageOrientationText": "Tra>Cor(-17.1)>Sag(1.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - 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"SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 622, - -7201, - -8762, - 694, - 63, - 15, - -20, - 5 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 233.337, - "WipMemBlock": "4eab4fa7-7458-46a2-a128-a8d024363841||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 9ff9ea4a8..000000000 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/26/v2/MD5E-s1103670--05ff7854ff54a5573e8762c0ec44795a.nii.gz/MD5E-s1103670--05ff7854ff54a5573e8762c0ec44795a.nii.gz \ No newline at end of file diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index f3c70095d..000000000 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:26:13.287500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999388, - 0.019371, - 0.0291166, - -0.00994255, - 0.955603, - -0.294491 - ], - "ImageOrientationText": "Tra>Cor(-17.1)>Sag(1.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0632438, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 622, - -7201, - -8762, - 694, - 63, - 15, - -20, - 5 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 233.337, - "WipMemBlock": "95e7a1b1-1073-4c87-a2c5-61fdcad354fe||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 3e51d92e8..000000000 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/74/G6/MD5E-s1103778--8b2cd7c35f901a0972434153978e05f0.nii.gz/MD5E-s1103778--8b2cd7c35f901a0972434153978e05f0.nii.gz \ No newline at end of file diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index 22243a6d6..000000000 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:35:53.040000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999388, - 0.019371, - 0.0291166, - -0.00994255, - 0.955603, - -0.294491 - ], - "ImageOrientationText": "Tra>Cor(-17.1)>Sag(1.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-05", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0632438, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 622, - -7201, - -8762, - 694, - 63, - 15, - -20, - 5 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 233.337, - "WipMemBlock": "fd520a17-1abc-4369-b6e6-2fd0a5f6cbb1||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index 7ef4e505e..000000000 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/fj/Wv/MD5E-s1103669--3f1cdcb2f71f67d3e6e5668fd4fdff4b.nii.gz/MD5E-s1103669--3f1cdcb2f71f67d3e6e5668fd4fdff4b.nii.gz \ No newline at end of file diff --git a/sub-03/ses-019/sub-03_ses-019_scans.tsv b/sub-03/ses-019/sub-03_ses-019_scans.tsv index be28190f7..be4d40c2d 120000 --- a/sub-03/ses-019/sub-03_ses-019_scans.tsv +++ b/sub-03/ses-019/sub-03_ses-019_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/2G/xK/MD5E-s3911--89d0f4ce889847b78b81c5b116e13a69.tsv/MD5E-s3911--89d0f4ce889847b78b81c5b116e13a69.tsv \ No newline at end of file +../../.git/annex/objects/q0/j5/MD5E-s3068--c7e205c02672cf79cf293e6147d3ab8c.tsv/MD5E-s3068--c7e205c02672cf79cf293e6147d3ab8c.tsv \ No newline at end of file From 325a3f0355534ee66a96c62a10a7bd676a63c6bc Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:57:07 -0400 Subject: [PATCH 382/463] fix complex event files --- ...g_events.tsv => sub-03_ses-001_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-03_ses-001_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-03_ses-001_task-mario3_run-03_events.tsv} | 0 .../func/sub-03_ses-001_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-03_ses-001_task-mario3_run-04_events.tsv} | 0 .../func/sub-03_ses-001_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-03_ses-001_task-mario3_run-04_part-phase_events.tsv | 1 - ...g_events.tsv => sub-03_ses-001_task-mario3_run-05_events.tsv} | 0 .../func/sub-03_ses-001_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-03_ses-001_task-mario3_run-05_part-phase_events.tsv | 1 - 10 files changed, 5 deletions(-) rename sub-03/ses-001/func/{sub-03_ses-001_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-001_task-mario3_run-01_events.tsv} (100%) rename sub-03/ses-001/func/{sub-03_ses-001_task-mario3_run-01_part-phase_events.tsv => sub-03_ses-001_task-mario3_run-02_events.tsv} (100%) rename sub-03/ses-001/func/{sub-03_ses-001_task-mario3_run-02_part-mag_events.tsv => sub-03_ses-001_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-03_part-phase_events.tsv rename sub-03/ses-001/func/{sub-03_ses-001_task-mario3_run-02_part-phase_events.tsv => sub-03_ses-001_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-04_part-phase_events.tsv rename sub-03/ses-001/func/{sub-03_ses-001_task-mario3_run-03_part-mag_events.tsv => sub-03_ses-001_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-05_part-phase_events.tsv diff --git a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-02_events.tsv similarity index 100% rename from sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-01_part-phase_events.tsv rename to sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-02_events.tsv diff --git a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-02_part-mag_events.tsv b/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-03_events.tsv similarity index 100% rename from sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-02_part-mag_events.tsv rename to sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-03_events.tsv diff --git a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-03_part-phase_events.tsv b/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-02_part-phase_events.tsv b/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-04_events.tsv similarity index 100% rename from sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-02_part-phase_events.tsv rename to sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-04_events.tsv diff --git a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-04_part-mag_events.tsv b/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-04_part-phase_events.tsv b/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-03_part-mag_events.tsv b/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-05_events.tsv similarity index 100% rename from sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-03_part-mag_events.tsv rename to sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-05_events.tsv diff --git a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-05_part-mag_events.tsv b/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-05_part-phase_events.tsv b/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 72aeec040629bc7ad99706e92cff15ae6dd17e3a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:57:19 -0400 Subject: [PATCH 383/463] fix complex event files --- ...g_events.tsv => sub-03_ses-019_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-03_ses-019_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-03_ses-019_task-mario3_run-03_events.tsv} | 0 .../func/sub-03_ses-019_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-03_ses-019_task-mario3_run-04_events.tsv} | 0 .../func/sub-03_ses-019_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-03_ses-019_task-mario3_run-04_part-phase_events.tsv | 1 - ...g_events.tsv => sub-03_ses-019_task-mario3_run-05_events.tsv} | 0 .../func/sub-03_ses-019_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-03_ses-019_task-mario3_run-05_part-phase_events.tsv | 1 - 10 files changed, 5 deletions(-) rename sub-03/ses-019/func/{sub-03_ses-019_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-019_task-mario3_run-01_events.tsv} (100%) rename sub-03/ses-019/func/{sub-03_ses-019_task-mario3_run-01_part-phase_events.tsv => sub-03_ses-019_task-mario3_run-02_events.tsv} (100%) rename sub-03/ses-019/func/{sub-03_ses-019_task-mario3_run-02_part-mag_events.tsv => sub-03_ses-019_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-03_part-phase_events.tsv rename sub-03/ses-019/func/{sub-03_ses-019_task-mario3_run-02_part-phase_events.tsv => sub-03_ses-019_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_part-phase_events.tsv rename sub-03/ses-019/func/{sub-03_ses-019_task-mario3_run-03_part-mag_events.tsv => sub-03_ses-019_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-phase_events.tsv diff --git a/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-02_events.tsv similarity index 100% rename from sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-01_part-phase_events.tsv rename to sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-02_events.tsv diff --git a/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-02_part-mag_events.tsv b/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-03_events.tsv similarity index 100% rename from sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-02_part-mag_events.tsv rename to sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-03_events.tsv diff --git a/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-03_part-phase_events.tsv b/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-02_part-phase_events.tsv b/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_events.tsv similarity index 100% rename from sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-02_part-phase_events.tsv rename to sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_events.tsv diff --git a/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_part-mag_events.tsv b/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_part-phase_events.tsv b/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-03_part-mag_events.tsv b/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_events.tsv similarity index 100% rename from sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-03_part-mag_events.tsv rename to sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_events.tsv diff --git a/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-mag_events.tsv b/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-phase_events.tsv b/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-019/func/sub-03_ses-019_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 4b4857d2dcc4a71ae6553c8bdd2baf900536fc37 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:57:21 -0400 Subject: [PATCH 384/463] fill IntendedFor --- ...3_ses-001_acq-sbref_dir-AP_run-01_epi.json | 92 +++---------------- ...3_ses-001_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...3_ses-001_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...3_ses-001_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...3_ses-001_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- ...3_ses-001_acq-sbref_dir-PA_run-05_epi.json | 88 ++---------------- 6 files changed, 46 insertions(+), 486 deletions(-) diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_epi.json index 4b62a5775..4c4904eae 100644 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999729, - 0.0102788, - 0.0209107, - -0.0043622, - 0.964136, - -0.265374 - ], + "ImageOrientationPatientDICOM": [0.999729, 0.0102788, 0.0209107, -0.0043622, 0.964136, -0.265374], "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,19 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-03_ses-001_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-001/func/sub-03_ses-001_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-001/func/sub-03_ses-001_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-001/func/sub-03_ses-001_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-001/func/sub-03_ses-001_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +67,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 642, - -7213, - -8768, - 706, - 82, - 31, - 47, - -17 - ], + "ShimSetting": [642, -7213, -8768, 706, 82, 31, 47, -17], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_epi.json index 67324492b..d72c176ae 100644 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999729, - 0.0102788, - 0.0209107, - -0.0043622, - 0.964136, - -0.265374 - ], + "ImageOrientationPatientDICOM": [0.999729, 0.0102788, 0.0209107, -0.0043622, 0.964136, -0.265374], "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-03_ses-001_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 642, - -7213, - -8768, - 706, - 82, - 31, - 47, - -17 - ], + "ShimSetting": [642, -7213, -8768, 706, 82, 31, 47, -17], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_epi.json index 36fe4e726..ded3ca318 100644 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999729, - 0.0102788, - 0.0209107, - -0.0043622, - 0.964136, - -0.265374 - ], + "ImageOrientationPatientDICOM": [0.999729, 0.0102788, 0.0209107, -0.0043622, 0.964136, -0.265374], "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-03_ses-001_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 642, - -7213, - -8768, - 706, - 82, - 31, - 47, - -17 - ], + "ShimSetting": [642, -7213, -8768, 706, 82, 31, 47, -17], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_epi.json index 16c3eceda..3e90594c1 100644 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999729, - 0.0102788, - 0.0209107, - -0.0043622, - 0.964136, - -0.265374 - ], + "ImageOrientationPatientDICOM": [0.999729, 0.0102788, 0.0209107, -0.0043622, 0.964136, -0.265374], "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-03_ses-001_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 642, - -7213, - -8768, - 706, - 82, - 31, - 47, - -17 - ], + "ShimSetting": [642, -7213, -8768, 706, 82, 31, 47, -17], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_epi.json index 25e3b7c35..cf9e100a8 100644 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999729, - 0.0102788, - 0.0209107, - -0.0043622, - 0.964136, - -0.265374 - ], + "ImageOrientationPatientDICOM": [0.999729, 0.0102788, 0.0209107, -0.0043622, 0.964136, -0.265374], "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-03_ses-001_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 642, - -7213, - -8768, - 706, - 82, - 31, - 47, - -17 - ], + "ShimSetting": [642, -7213, -8768, 706, 82, 31, 47, -17], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.02, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_epi.json b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_epi.json index 1a1f898df..27bc94c71 100644 --- a/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-03/ses-001/fmap/sub-03_ses-001_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999729, - 0.0102788, - 0.0209107, - -0.0043622, - 0.964136, - -0.265374 - ], + "ImageOrientationPatientDICOM": [0.999729, 0.0102788, 0.0209107, -0.0043622, 0.964136, -0.265374], "ImageOrientationText": "Tra>Cor(-15.4)>Sag(1.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-03_ses-001_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 642, - -7213, - -8768, - 706, - 82, - 31, - 47, - -17 - ], + "ShimSetting": [642, -7213, -8768, 706, 82, 31, 47, -17], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 043a0b71baf1320b30ece66000ced74075fe1188 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:57:33 -0400 Subject: [PATCH 385/463] fill IntendedFor --- ...3_ses-019_acq-sbref_dir-AP_run-01_epi.json | 92 +++---------------- ...3_ses-019_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...3_ses-019_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...3_ses-019_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...3_ses-019_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- ...3_ses-019_acq-sbref_dir-PA_run-05_epi.json | 88 ++---------------- 6 files changed, 46 insertions(+), 486 deletions(-) diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_epi.json index f8de9d76e..f32c092e8 100644 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999388, - 0.019371, - 0.0291166, - -0.00994255, - 0.955603, - -0.294491 - ], + "ImageOrientationPatientDICOM": [0.999388, 0.019371, 0.0291166, -0.00994255, 0.955603, -0.294491], "ImageOrientationText": "Tra>Cor(-17.1)>Sag(1.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,19 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-019/func/sub-03_ses-019_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-019/func/sub-03_ses-019_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-019/func/sub-03_ses-019_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-019/func/sub-03_ses-019_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-019/func/sub-03_ses-019_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +67,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 622, - -7201, - -8762, - 694, - 63, - 15, - -20, - 5 - ], + "ShimSetting": [622, -7201, -8762, 694, 63, 15, -20, 5], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_epi.json index ce9ce6cbf..26eba291d 100644 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999388, - 0.019371, - 0.0291166, - -0.00994255, - 0.955603, - -0.294491 - ], + "ImageOrientationPatientDICOM": [0.999388, 0.019371, 0.0291166, -0.00994255, 0.955603, -0.294491], "ImageOrientationText": "Tra>Cor(-17.1)>Sag(1.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-019/func/sub-03_ses-019_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 622, - -7201, - -8762, - 694, - 63, - 15, - -20, - 5 - ], + "ShimSetting": [622, -7201, -8762, 694, 63, 15, -20, 5], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_epi.json index dc3159f8d..182404ec9 100644 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999388, - 0.019371, - 0.0291166, - -0.00994255, - 0.955603, - -0.294491 - ], + "ImageOrientationPatientDICOM": [0.999388, 0.019371, 0.0291166, -0.00994255, 0.955603, -0.294491], "ImageOrientationText": "Tra>Cor(-17.1)>Sag(1.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-019/func/sub-03_ses-019_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 622, - -7201, - -8762, - 694, - 63, - 15, - -20, - 5 - ], + "ShimSetting": [622, -7201, -8762, 694, 63, 15, -20, 5], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_epi.json index dceb0413a..6d7fb574a 100644 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999388, - 0.019371, - 0.0291166, - -0.00994255, - 0.955603, - -0.294491 - ], + "ImageOrientationPatientDICOM": [0.999388, 0.019371, 0.0291166, -0.00994255, 0.955603, -0.294491], "ImageOrientationText": "Tra>Cor(-17.1)>Sag(1.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-019/func/sub-03_ses-019_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 622, - -7201, - -8762, - 694, - 63, - 15, - -20, - 5 - ], + "ShimSetting": [622, -7201, -8762, 694, 63, 15, -20, 5], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_epi.json index 33d01c8e3..9a2cb403f 100644 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999388, - 0.019371, - 0.0291166, - -0.00994255, - 0.955603, - -0.294491 - ], + "ImageOrientationPatientDICOM": [0.999388, 0.019371, 0.0291166, -0.00994255, 0.955603, -0.294491], "ImageOrientationText": "Tra>Cor(-17.1)>Sag(1.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-019/func/sub-03_ses-019_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 622, - -7201, - -8762, - 694, - 63, - 15, - -20, - 5 - ], + "ShimSetting": [622, -7201, -8762, 694, 63, 15, -20, 5], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_epi.json b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_epi.json index 661b65902..3216d319d 100644 --- a/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-03/ses-019/fmap/sub-03_ses-019_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999388, - 0.019371, - 0.0291166, - -0.00994255, - 0.955603, - -0.294491 - ], + "ImageOrientationPatientDICOM": [0.999388, 0.019371, 0.0291166, -0.00994255, 0.955603, -0.294491], "ImageOrientationText": "Tra>Cor(-17.1)>Sag(1.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-019/func/sub-03_ses-019_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 622, - -7201, - -8762, - 694, - 63, - 15, - -20, - 5 - ], + "ShimSetting": [622, -7201, -8762, 694, 63, 15, -20, 5], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 916f42454e10a654d303e4204eabfbcf6994e94f Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 17:59:24 -0400 Subject: [PATCH 386/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..934cca3fa --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = ad942887-bf31-4f0f-8fc0-21daeda15fb0 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..9fa5ac3d7 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 9fa5ac3d799c92ca18f745a12022daff5371a400 From 1656641ace9633d8a454e2c23d07f46b67fcdc8a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 18:00:17 -0400 Subject: [PATCH 387/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..b64d068b8 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 4c0d6f11-f0a6-4221-96b7-3aca46eeff9b diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..7e3bad2d9 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 7e3bad2d98bec33d4d16544c3653690a47ce8104 From 1b6ba9304c37c49c241ad230ead114ac331fc451 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 18:00:27 -0400 Subject: [PATCH 388/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-05_ses-002_acq-axial_localizer.json | 81 +++ .../sub-05_ses-002_acq-axial_localizer.nii.gz | 1 + .../sub-05_ses-002_acq-coronal_localizer.json | 81 +++ ...ub-05_ses-002_acq-coronal_localizer.nii.gz | 1 + ...sub-05_ses-002_acq-sagittal_localizer.json | 86 +++ ...b-05_ses-002_acq-sagittal_localizer.nii.gz | 1 + sub-05/ses-002/anat/sub-05_ses-002_scout.json | 542 ++++++++++++++++++ .../ses-002/anat/sub-05_ses-002_scout.nii.gz | 1 + ...2_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-06_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-06_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-07_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-07_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-07_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-07_part-phase_epi.nii.gz | 1 + ...-002_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-01_part-mag_events.tsv | 1 + ...002_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-01_part-phase_events.tsv | 1 + ...2_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-002_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-02_part-mag_events.tsv | 1 + ...002_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-02_part-phase_events.tsv | 1 + ...2_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-002_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-03_part-mag_events.tsv | 1 + ...002_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-03_part-phase_events.tsv | 1 + ...2_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-002_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-04_part-mag_events.tsv | 1 + ...002_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-04_part-phase_events.tsv | 1 + ...2_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-002_task-mario3_run-05_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-05_part-mag_events.tsv | 1 + ...002_task-mario3_run-05_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-05_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-05_part-phase_events.tsv | 1 + ...2_task-mario3_run-05_part-phase_sbref.json | 153 +++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + ...-002_task-mario3_run-06_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-06_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-06_part-mag_events.tsv | 1 + ...002_task-mario3_run-06_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-06_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-06_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-06_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-06_part-phase_events.tsv | 1 + ...2_task-mario3_run-06_part-phase_sbref.json | 153 +++++ ...task-mario3_run-06_part-phase_sbref.nii.gz | 1 + ...-002_task-mario3_run-07_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-07_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-07_part-mag_events.tsv | 1 + ...002_task-mario3_run-07_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-07_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-07_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-07_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-07_part-phase_events.tsv | 1 + ...2_task-mario3_run-07_part-phase_sbref.json | 153 +++++ ...task-mario3_run-07_part-phase_sbref.nii.gz | 1 + sub-05/ses-002/sub-05_ses-002_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 121 files changed, 8295 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-05/ses-002/anat/sub-05_ses-002_acq-axial_localizer.json create mode 120000 sub-05/ses-002/anat/sub-05_ses-002_acq-axial_localizer.nii.gz create mode 100644 sub-05/ses-002/anat/sub-05_ses-002_acq-coronal_localizer.json create mode 120000 sub-05/ses-002/anat/sub-05_ses-002_acq-coronal_localizer.nii.gz create mode 100644 sub-05/ses-002/anat/sub-05_ses-002_acq-sagittal_localizer.json create mode 120000 sub-05/ses-002/anat/sub-05_ses-002_acq-sagittal_localizer.nii.gz create mode 100644 sub-05/ses-002/anat/sub-05_ses-002_scout.json create mode 120000 sub-05/ses-002/anat/sub-05_ses-002_scout.nii.gz create mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_part-mag_epi.json create mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz create mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_part-phase_epi.json create mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz create mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_part-mag_epi.json create mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz create mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_part-phase_epi.json create mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz create mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_part-mag_epi.json create mode 120000 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sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-05_part-phase_events.tsv create mode 100644 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-05_part-phase_sbref.json create mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-05_part-phase_sbref.nii.gz create mode 100644 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_part-mag_bold.json create mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_part-mag_bold.nii.gz create mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_part-mag_events.tsv create mode 100644 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_part-mag_sbref.json create mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_part-mag_sbref.nii.gz create mode 100644 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_part-phase_bold.json create mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_part-phase_bold.nii.gz create mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_part-phase_events.tsv create mode 100644 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_part-phase_sbref.json create mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_part-phase_sbref.nii.gz create mode 100644 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_part-mag_bold.json create mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_part-mag_bold.nii.gz create mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_part-mag_events.tsv create mode 100644 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_part-mag_sbref.json create mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_part-mag_sbref.nii.gz create mode 100644 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_part-phase_bold.json create mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_part-phase_bold.nii.gz create mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_part-phase_events.tsv create mode 100644 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_part-phase_sbref.json create mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_part-phase_sbref.nii.gz create mode 120000 sub-05/ses-002/sub-05_ses-002_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 9fa5ac3d7..3517d6a22 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 9fa5ac3d799c92ca18f745a12022daff5371a400 +Subproject commit 3517d6a22165f3c8c11e101279feb40f37611003 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..adca14c3c --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-05 51 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-05/ses-002/anat/sub-05_ses-002_acq-axial_localizer.json b/sub-05/ses-002/anat/sub-05_ses-002_acq-axial_localizer.json new file mode 100644 index 000000000..d4a9acc7f --- /dev/null +++ b/sub-05/ses-002/anat/sub-05_ses-002_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:29:17.040000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": 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"MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0571011, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [591, -7251, -8832, 449, 14, -302, 16, 26], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 262.255, + "dcmmeta_affine": [ + [-1.9945977926254272, 0.1408751755952835, -0.041636791080236435, 97.85974884033203], + [0.1467851847410202, 1.8889634609222412, -0.64052414894104, -75.07450103759766], + [0.005791783798485994, 0.6418498754501343, 1.8942004442214966, -58.9144287109375], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From e94003be74a4ff1ae2c030267a24a079c5b248bc Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 18:01:03 -0400 Subject: [PATCH 389/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-018_acq-axial_localizer.json | 81 +++ .../sub-02_ses-018_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-018_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-018_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-018_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-018_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-018/anat/sub-02_ses-018_scout.json | 542 ++++++++++++++++++ .../ses-018/anat/sub-02_ses-018_scout.nii.gz | 1 + ...8_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-06_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-06_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 + ...-018_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...18_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...018_task-mario3_run-01_part-mag_events.tsv | 1 + ...018_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...18_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-01_part-phase_events.tsv | 1 + ...8_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-018_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...18_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...018_task-mario3_run-02_part-mag_events.tsv | 1 + ...018_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...18_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-02_part-phase_events.tsv | 1 + ...8_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-018_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...18_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...018_task-mario3_run-03_part-mag_events.tsv | 1 + ...018_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...18_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-03_part-phase_events.tsv | 1 + ...8_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-018_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...18_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...018_task-mario3_run-04_part-mag_events.tsv | 1 + ...018_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...18_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-04_part-phase_events.tsv | 1 + ...8_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-018_task-mario3_run-05_part-mag_bold.json | 172 ++++++ ...18_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...018_task-mario3_run-05_part-mag_events.tsv | 1 + ...018_task-mario3_run-05_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...18_task-mario3_run-05_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-05_part-phase_events.tsv | 1 + ...8_task-mario3_run-05_part-phase_sbref.json | 153 +++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + ...-018_task-mario3_run-06_part-mag_bold.json | 172 ++++++ ...18_task-mario3_run-06_part-mag_bold.nii.gz | 1 + ...018_task-mario3_run-06_part-mag_events.tsv | 1 + ...018_task-mario3_run-06_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-06_part-mag_sbref.nii.gz | 1 + ...18_task-mario3_run-06_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-06_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-06_part-phase_events.tsv | 1 + ...8_task-mario3_run-06_part-phase_sbref.json | 153 +++++ ...task-mario3_run-06_part-phase_sbref.nii.gz | 1 + sub-02/ses-018/sub-02_ses-018_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 107 files changed, 7333 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-018/anat/sub-02_ses-018_acq-axial_localizer.json create mode 120000 sub-02/ses-018/anat/sub-02_ses-018_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-018/anat/sub-02_ses-018_acq-coronal_localizer.json create mode 120000 sub-02/ses-018/anat/sub-02_ses-018_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-018/anat/sub-02_ses-018_acq-sagittal_localizer.json create mode 120000 sub-02/ses-018/anat/sub-02_ses-018_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-018/anat/sub-02_ses-018_scout.json create mode 120000 sub-02/ses-018/anat/sub-02_ses-018_scout.nii.gz create mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_part-mag_epi.json create mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz create mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_part-phase_epi.json create mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz create mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_part-mag_epi.json create mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz create mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_part-phase_epi.json create mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_part-mag_bold.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_part-mag_bold.nii.gz create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_part-mag_events.tsv create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_part-mag_sbref.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_part-phase_bold.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_part-phase_bold.nii.gz create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_part-phase_events.tsv create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_part-phase_sbref.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-mag_bold.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-mag_bold.nii.gz create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-mag_events.tsv create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-mag_sbref.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-phase_bold.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-phase_bold.nii.gz create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-phase_events.tsv create mode 100644 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-phase_sbref.json create mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-phase_sbref.nii.gz create mode 120000 sub-02/ses-018/sub-02_ses-018_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 7e3bad2d9..10bff0eec 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 7e3bad2d98bec33d4d16544c3653690a47ce8104 +Subproject commit 10bff0eecf77c3a204799374f82261ef52b6fc4b diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..83ada7a9d --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 51 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-018/anat/sub-02_ses-018_acq-axial_localizer.json b/sub-02/ses-018/anat/sub-02_ses-018_acq-axial_localizer.json new file mode 100644 index 000000000..322b0c534 --- /dev/null +++ b/sub-02/ses-018/anat/sub-02_ses-018_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:37:26.035000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + 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000000000..65b92b762 --- /dev/null +++ b/sub-02/ses-018/anat/sub-02_ses-018_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Z0/kj/MD5E-s184302--4eabb7b1043beca82ad9d89221ce3bf7.nii.gz/MD5E-s184302--4eabb7b1043beca82ad9d89221ce3bf7.nii.gz \ No newline at end of file diff --git a/sub-02/ses-018/anat/sub-02_ses-018_acq-coronal_localizer.json b/sub-02/ses-018/anat/sub-02_ses-018_acq-coronal_localizer.json new file mode 100644 index 000000000..3b5dfe530 --- /dev/null +++ b/sub-02/ses-018/anat/sub-02_ses-018_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:37:33.025000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + 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b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-phase_events.tsv new file mode 120000 index 000000000..1bbdfddb5 --- /dev/null +++ b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-phase_events.tsv @@ -0,0 +1 @@ +../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-phase_sbref.json b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-phase_sbref.json new file mode 100644 index 000000000..513bd7128 --- /dev/null +++ b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-phase_sbref.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "16:35:25.365000", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": 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+ "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0444002, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [618, -7192, -8865, 262, 5, -162, -11, 45], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 251.275, + "dcmmeta_affine": [ + [-1.9964444637298584, 0.03205959126353264, 0.11481092870235443, 102.78025817871094], + [-0.028491513803601265, 1.7421371936798096, -0.981909453868866, -50.029693603515625], + [0.11574799567461014, 0.9817994236946106, 1.7385834455490112, -96.4617919921875], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 327f0fa6e27ed8bd48490a408b5e4a46976de3cb Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 18:01:32 -0400 Subject: [PATCH 390/463] fix fmap phase --- ...5_ses-002_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-002_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-002_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-06_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-06_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-07_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-07_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-07_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-07_part-phase_epi.nii.gz | 1 - sub-05/ses-002/sub-05_ses-002_scans.tsv | 2 +- 37 files changed, 1 insertion(+), 1403 deletions(-) rename sub-05/ses-002/fmap/{sub-05_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-05_ses-002_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-002/fmap/{sub-05_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-002_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-002/fmap/{sub-05_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-05_ses-002_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-002/fmap/{sub-05_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-002_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-002/fmap/{sub-05_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-05_ses-002_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-05/ses-002/fmap/{sub-05_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-05_ses-002_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-05/ses-002/fmap/{sub-05_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-05_ses-002_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-05/ses-002/fmap/{sub-05_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-05_ses-002_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-05/ses-002/fmap/{sub-05_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-05_ses-002_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-05/ses-002/fmap/{sub-05_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-05_ses-002_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-05/ses-002/fmap/{sub-05_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-05_ses-002_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-05/ses-002/fmap/{sub-05_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-05_ses-002_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-05/ses-002/fmap/{sub-05_ses-002_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-05_ses-002_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-05/ses-002/fmap/{sub-05_ses-002_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-05_ses-002_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz rename sub-05/ses-002/fmap/{sub-05_ses-002_acq-sbref_dir-PA_run-06_part-mag_epi.json => sub-05_ses-002_acq-sbref_dir-PA_run-06_epi.json} (100%) rename sub-05/ses-002/fmap/{sub-05_ses-002_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz => sub-05_ses-002_acq-sbref_dir-PA_run-06_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_part-phase_epi.json delete mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz rename sub-05/ses-002/fmap/{sub-05_ses-002_acq-sbref_dir-PA_run-07_part-mag_epi.json => sub-05_ses-002_acq-sbref_dir-PA_run-07_epi.json} (100%) rename sub-05/ses-002/fmap/{sub-05_ses-002_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz => sub-05_ses-002_acq-sbref_dir-PA_run-07_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_part-phase_epi.json delete mode 120000 sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index b83efeaaa..000000000 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:31:20.777500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 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"slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["183120.777500", "183122.267500", "183123.757500"], - "ContentTime": ["183206.371000", "183206.374000", "183206.376000"], - "InstanceCreationTime": ["183206.371000", "183206.374000", "183206.376000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4966.0, 4944.0, 4942.0], - "WindowWidth": [18780.0, 18744.0, 18742.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 397d18834..000000000 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/KG/JZ/MD5E-s3334155--895bf204805064cbe2adb3b98db6d821.nii.gz/MD5E-s3334155--895bf204805064cbe2adb3b98db6d821.nii.gz \ No newline at end of file diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 4cd776154..000000000 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:31:10.347500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997299, - -0.0733926, - 0.00289589, - 0.0704376, - 0.944482, - -0.320925 - ], - "ImageOrientationText": "Tra>Cor(-18.7)>Sag(-1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0455383, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 591, - -7251, - -8832, - 449, - 14, - -302, - 16, - 26 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.51, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 262.255, - "WipMemBlock": "31339b11-e13e-408c-939c-4b9afdf0236d||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 23aa88f8a..000000000 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/w3/m8/MD5E-s1112212--20f027449d37c03bc47b89aa3d3fa3ef.nii.gz/MD5E-s1112212--20f027449d37c03bc47b89aa3d3fa3ef.nii.gz \ No newline at end of file diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 03d87ea1a..000000000 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:35:55.945000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": 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b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index cf9ee01f7..000000000 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Qf/10/MD5E-s1103543--9b4fd719c16833e259846404c32e483f.nii.gz/MD5E-s1103543--9b4fd719c16833e259846404c32e483f.nii.gz \ No newline at end of file diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 58ef2cfbf..000000000 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:49:1.992500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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"PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0571011, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 591, - -7251, - -8832, - 449, - 14, - -302, - 16, - 26 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 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-../../../.git/annex/objects/7Z/g7/MD5E-s1103503--7f31865cfefe9246a2b73eedab8ceb57.nii.gz/MD5E-s1103503--7f31865cfefe9246a2b73eedab8ceb57.nii.gz \ No newline at end of file diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 046c91b64..000000000 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:57:58.592500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 262.255, - "WipMemBlock": "fc8aab16-a70d-4116-916b-270cf6d007f4||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 1e76bda4b..000000000 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/xW/vw/MD5E-s1103599--76f0f05fe94d45d0e7d2df1057ecfe84.nii.gz/MD5E-s1103599--76f0f05fe94d45d0e7d2df1057ecfe84.nii.gz \ No newline at end of file diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 066244c1c..000000000 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:09:30.120000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997299, - -0.0733926, - 0.00289589, - 0.0704376, - 0.944482, - -0.320925 - ], - "ImageOrientationText": "Tra>Cor(-18.7)>Sag(-1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - 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"afbf8ac8-a61b-46ee-9b8e-72f7b1256349||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index c4ba94c7a..000000000 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/F6/0m/MD5E-s1103414--448ec14a01ea9cc8e10c2ecdd9b1d9ff.nii.gz/MD5E-s1103414--448ec14a01ea9cc8e10c2ecdd9b1d9ff.nii.gz \ No newline at end of file diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index 3765cf67a..000000000 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:18:42.635000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of 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"MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-05", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0571011, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 591, - -7251, - -8832, - 449, - 14, - -302, - 16, - 26 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 262.255, - "WipMemBlock": "9f3daa7c-d382-4d8a-9ef6-49910df8a0c8||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index b407e9d21..000000000 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/4x/0x/MD5E-s1103544--cf8e98273b1e704b9136cc208ef969f1.nii.gz/MD5E-s1103544--cf8e98273b1e704b9136cc208ef969f1.nii.gz \ No newline at end of file diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_part-mag_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_epi.json similarity index 100% rename from sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_part-mag_epi.json rename to sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_epi.json diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_epi.nii.gz similarity index 100% rename from sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz rename to sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_epi.nii.gz diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_part-phase_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_part-phase_epi.json deleted file mode 100644 index f39fee3b4..000000000 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:34:57.152500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997299, - -0.0733926, - 0.00289589, - 0.0704376, - 0.944482, - -0.320925 - ], - "ImageOrientationText": "Tra>Cor(-18.7)>Sag(-1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-06", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0571011, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-06_SBRef", - "SeriesNumber": 24, - "ShimSetting": [ - 591, - -7251, - -8832, - 449, - 14, - -302, - 16, - 26 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 262.255, - "WipMemBlock": "c4831f5e-f249-4575-9597-f4d311e07821||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz deleted file mode 120000 index 16adbda61..000000000 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/J1/5X/MD5E-s1103629--7330cf5c9492340175075e19d2b4f67f.nii.gz/MD5E-s1103629--7330cf5c9492340175075e19d2b4f67f.nii.gz \ No newline at end of file diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_part-mag_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_epi.json similarity index 100% rename from sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_part-mag_epi.json rename to sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_epi.json diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_epi.nii.gz similarity index 100% rename from sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz rename to sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_epi.nii.gz diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_part-phase_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_part-phase_epi.json deleted file mode 100644 index 15655e7aa..000000000 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:49:31.212500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997299, - -0.0733926, - 0.00289589, - 0.0704376, - 0.944482, - -0.320925 - ], - "ImageOrientationText": "Tra>Cor(-18.7)>Sag(-1.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-07", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0571011, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-07_SBRef", - "SeriesNumber": 27, - "ShimSetting": [ - 591, - -7251, - -8832, - 449, - 14, - -302, - 16, - 26 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 262.255, - "WipMemBlock": "dd373d17-a300-4f02-81e9-cf5730e4664a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz deleted file mode 120000 index 68ee214a2..000000000 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/x4/58/MD5E-s1103572--4a9ba412dca8a41c3bf3394bf7084b80.nii.gz/MD5E-s1103572--4a9ba412dca8a41c3bf3394bf7084b80.nii.gz \ No newline at end of file diff --git a/sub-05/ses-002/sub-05_ses-002_scans.tsv b/sub-05/ses-002/sub-05_ses-002_scans.tsv index 951979007..87d81a871 120000 --- a/sub-05/ses-002/sub-05_ses-002_scans.tsv +++ b/sub-05/ses-002/sub-05_ses-002_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/wp/P2/MD5E-s5155--29165fe9b3f9f47492b4ce7178f7677c.tsv/MD5E-s5155--29165fe9b3f9f47492b4ce7178f7677c.tsv \ No newline at end of file +../../.git/annex/objects/kX/vk/MD5E-s4070--46c4cbbc27aac2360e4030c47a66bd53.tsv/MD5E-s4070--46c4cbbc27aac2360e4030c47a66bd53.tsv \ No newline at end of file From 73a7c5aeea5862683f3a99e0c5d0e25b6c3d46fb Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 18:01:49 -0400 Subject: [PATCH 391/463] fix complex event files --- ...g_events.tsv => sub-05_ses-002_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-05_ses-002_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-05_ses-002_task-mario3_run-03_events.tsv} | 0 ...e_events.tsv => sub-05_ses-002_task-mario3_run-04_events.tsv} | 0 .../func/sub-05_ses-002_task-mario3_run-04_part-phase_events.tsv | 1 - ...g_events.tsv => sub-05_ses-002_task-mario3_run-05_events.tsv} | 0 .../func/sub-05_ses-002_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-05_ses-002_task-mario3_run-05_part-phase_events.tsv | 1 - ...e_events.tsv => sub-05_ses-002_task-mario3_run-06_events.tsv} | 0 .../func/sub-05_ses-002_task-mario3_run-06_part-mag_events.tsv | 1 - .../func/sub-05_ses-002_task-mario3_run-06_part-phase_events.tsv | 1 - ...g_events.tsv => sub-05_ses-002_task-mario3_run-07_events.tsv} | 0 .../func/sub-05_ses-002_task-mario3_run-07_part-mag_events.tsv | 1 - .../func/sub-05_ses-002_task-mario3_run-07_part-phase_events.tsv | 1 - 14 files changed, 7 deletions(-) rename sub-05/ses-002/func/{sub-05_ses-002_task-mario3_run-01_part-mag_events.tsv => sub-05_ses-002_task-mario3_run-01_events.tsv} (100%) rename sub-05/ses-002/func/{sub-05_ses-002_task-mario3_run-01_part-phase_events.tsv => sub-05_ses-002_task-mario3_run-02_events.tsv} (100%) rename sub-05/ses-002/func/{sub-05_ses-002_task-mario3_run-02_part-mag_events.tsv => sub-05_ses-002_task-mario3_run-03_events.tsv} (100%) rename sub-05/ses-002/func/{sub-05_ses-002_task-mario3_run-02_part-phase_events.tsv => sub-05_ses-002_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-04_part-phase_events.tsv rename sub-05/ses-002/func/{sub-05_ses-002_task-mario3_run-03_part-mag_events.tsv => sub-05_ses-002_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-05_part-phase_events.tsv rename sub-05/ses-002/func/{sub-05_ses-002_task-mario3_run-03_part-phase_events.tsv => sub-05_ses-002_task-mario3_run-06_events.tsv} (100%) delete mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_part-mag_events.tsv delete mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_part-phase_events.tsv rename sub-05/ses-002/func/{sub-05_ses-002_task-mario3_run-04_part-mag_events.tsv => sub-05_ses-002_task-mario3_run-07_events.tsv} (100%) delete mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_part-mag_events.tsv delete mode 120000 sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_part-phase_events.tsv diff --git a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-01_part-mag_events.tsv b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-01_events.tsv similarity index 100% rename from sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-01_part-mag_events.tsv rename to sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-01_events.tsv diff --git a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-01_part-phase_events.tsv b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-02_events.tsv similarity index 100% rename from sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-01_part-phase_events.tsv rename to sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-02_events.tsv diff --git a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-02_part-mag_events.tsv b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-03_events.tsv similarity index 100% rename from sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-02_part-mag_events.tsv rename to sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-03_events.tsv diff --git a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-02_part-phase_events.tsv b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-04_events.tsv similarity index 100% rename from sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-02_part-phase_events.tsv rename to sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-04_events.tsv diff --git a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-04_part-phase_events.tsv b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-03_part-mag_events.tsv b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-05_events.tsv similarity index 100% rename from sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-03_part-mag_events.tsv rename to sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-05_events.tsv diff --git a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-05_part-mag_events.tsv b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-05_part-phase_events.tsv b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-03_part-phase_events.tsv b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_events.tsv similarity index 100% rename from sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-03_part-phase_events.tsv rename to sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_events.tsv diff --git a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_part-mag_events.tsv b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_part-phase_events.tsv b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-06_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-04_part-mag_events.tsv b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_events.tsv similarity index 100% rename from sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-04_part-mag_events.tsv rename to sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_events.tsv diff --git a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_part-mag_events.tsv b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_part-phase_events.tsv b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-07_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From cc7cc41d318a51af77fce8223864e52a54cfaef9 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 18:02:05 -0400 Subject: [PATCH 392/463] fix fmap phase --- ...2_ses-018_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-018_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-018_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-018_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-018_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-018_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-018_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-018_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - ..._ses-018_acq-sbref_dir-PA_run-06_epi.json} | 0 ...es-018_acq-sbref_dir-PA_run-06_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 - sub-02/ses-018/sub-02_ses-018_scans.tsv | 2 +- 33 files changed, 1 insertion(+), 1250 deletions(-) rename sub-02/ses-018/fmap/{sub-02_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-018_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-018/fmap/{sub-02_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-018_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-018/fmap/{sub-02_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-018_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-018/fmap/{sub-02_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-018_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-018/fmap/{sub-02_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-018_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-018/fmap/{sub-02_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-018_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-018/fmap/{sub-02_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-018_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-018/fmap/{sub-02_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-018_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-018/fmap/{sub-02_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-018_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-018/fmap/{sub-02_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-018_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-02/ses-018/fmap/{sub-02_ses-018_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-02_ses-018_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-02/ses-018/fmap/{sub-02_ses-018_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-02_ses-018_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-02/ses-018/fmap/{sub-02_ses-018_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-02_ses-018_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-02/ses-018/fmap/{sub-02_ses-018_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-02_ses-018_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz rename sub-02/ses-018/fmap/{sub-02_ses-018_acq-sbref_dir-PA_run-06_part-mag_epi.json => sub-02_ses-018_acq-sbref_dir-PA_run-06_epi.json} (100%) rename sub-02/ses-018/fmap/{sub-02_ses-018_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz => sub-02_ses-018_acq-sbref_dir-PA_run-06_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_part-phase_epi.json delete mode 120000 sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 9be47d9cc..000000000 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:38:28.017500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - 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"RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.03540936092341, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "153913.349000", - "SliceLocation": -53.390975476559, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.000000028934, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "145355.839000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["153828.017500", "153829.507500", "153830.997500"], - "ContentTime": ["153913.351000", "153913.353000", "153913.356000"], - "InstanceCreationTime": ["153913.351000", "153913.353000", "153913.356000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4928.0, 4916.0, 4926.0], - "WindowWidth": [18734.0, 18744.0, 18736.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 037346d08..000000000 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/J0/Jq/MD5E-s3333278--7df71b4860a892a973052f8a5b16f1c7.nii.gz/MD5E-s3333278--7df71b4860a892a973052f8a5b16f1c7.nii.gz \ No newline at end of file diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index c1d63e77e..000000000 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:38:17.587500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998222, - 0.0142458, - 0.057874, - 0.0160298, - 0.871069, - -0.4909 - ], - "ImageOrientationText": "Tra>Cor(-29.5)>Sag(3.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - 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0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.51, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.275, - "WipMemBlock": "09ef4eb0-0628-440f-be40-15e0282db0a4||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 8f85e3286..000000000 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/1Z/jV/MD5E-s1112002--2ce5d91a44a350147a80374eaaef6d28.nii.gz/MD5E-s1112002--2ce5d91a44a350147a80374eaaef6d28.nii.gz \ No newline at end of file diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index afe8afcb3..000000000 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:40:3.312500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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"PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0444002, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 618, - -7192, - -8865, - 262, - 5, - -162, - -11, - 45 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.275, - "WipMemBlock": "d3cfe07e-66f1-4bb6-aeb2-0e73cc6327ba||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 0c393b808..000000000 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/21/6V/MD5E-s1103343--7169542ce0ff1b8f2ff604c90862de74.nii.gz/MD5E-s1103343--7169542ce0ff1b8f2ff604c90862de74.nii.gz \ No newline at end of file diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 9acf79243..000000000 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:53:54.142500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998222, - 0.0142458, - 0.057874, - 0.0160298, - 0.871069, - -0.4909 - ], - "ImageOrientationText": "Tra>Cor(-29.5)>Sag(3.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0444002, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 618, - -7192, - -8865, - 262, - 5, - -162, - -11, - 45 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.275, - "WipMemBlock": "fed9f623-5db9-47bb-9e5f-706b22d6bcad||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index b76d73f5a..000000000 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/WX/gj/MD5E-s1103158--e0afb58abaf822296bee815e56a3ad85.nii.gz/MD5E-s1103158--e0afb58abaf822296bee815e56a3ad85.nii.gz \ No newline at end of file diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index acf839ade..000000000 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:06:9.630000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998222, - 0.0142458, - 0.057874, - 0.0160298, - 0.871069, - -0.4909 - ], - "ImageOrientationText": "Tra>Cor(-29.5)>Sag(3.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0444002, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 618, - -7192, - -8865, - 262, - 5, - -162, - -11, - 45 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.275, - "WipMemBlock": "0fc282ba-2589-4008-ae9c-112627737d25||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index e673180c5..000000000 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/FF/02/MD5E-s1103421--8ef83290aa473fa680c8618827fd1648.nii.gz/MD5E-s1103421--8ef83290aa473fa680c8618827fd1648.nii.gz \ No newline at end of file diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index d72552c09..000000000 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:16:28.115000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998222, - 0.0142458, - 0.057874, - 0.0160298, - 0.871069, - -0.4909 - ], - "ImageOrientationText": "Tra>Cor(-29.5)>Sag(3.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0444002, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 618, - -7192, - -8865, - 262, - 5, - -162, - -11, - 45 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.275, - "WipMemBlock": "dd127877-c2fb-4bf1-a90d-ae77b77651c1||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 4b1f16866..000000000 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/gK/9k/MD5E-s1103410--0caaa6daee2dc2c5d984aa7e5445957b.nii.gz/MD5E-s1103410--0caaa6daee2dc2c5d984aa7e5445957b.nii.gz \ No newline at end of file diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index b43fdcaf1..000000000 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:25:35.070000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998222, - 0.0142458, - 0.057874, - 0.0160298, - 0.871069, - -0.4909 - ], - "ImageOrientationText": "Tra>Cor(-29.5)>Sag(3.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-05", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0444002, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 618, - -7192, - -8865, - 262, - 5, - -162, - -11, - 45 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.275, - "WipMemBlock": "7d06d0d3-d1f8-4cba-87fc-29848f7bc701||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index 78f82bdba..000000000 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/4Z/3F/MD5E-s1103146--6690607f8252c22bdc72f8069ac46325.nii.gz/MD5E-s1103146--6690607f8252c22bdc72f8069ac46325.nii.gz \ No newline at end of file diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_part-mag_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_epi.json similarity index 100% rename from sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_part-mag_epi.json rename to sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_epi.json diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_epi.nii.gz similarity index 100% rename from sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz rename to sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_epi.nii.gz diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_part-phase_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_part-phase_epi.json deleted file mode 100644 index bd987abea..000000000 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:35:25.365000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998222, - 0.0142458, - 0.057874, - 0.0160298, - 0.871069, - -0.4909 - ], - "ImageOrientationText": "Tra>Cor(-29.5)>Sag(3.3)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-06", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0444002, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-06_SBRef", - "SeriesNumber": 24, - "ShimSetting": [ - 618, - -7192, - -8865, - 262, - 5, - -162, - -11, - 45 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.275, - "WipMemBlock": "621e203d-95e7-4e19-bd35-e1187dd594ed||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz deleted file mode 120000 index 630e2f33b..000000000 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/kM/02/MD5E-s1103355--c828d609335a77409a6c2de9dad1d2a1.nii.gz/MD5E-s1103355--c828d609335a77409a6c2de9dad1d2a1.nii.gz \ No newline at end of file diff --git a/sub-02/ses-018/sub-02_ses-018_scans.tsv b/sub-02/ses-018/sub-02_ses-018_scans.tsv index 77ea03178..56ef51923 120000 --- a/sub-02/ses-018/sub-02_ses-018_scans.tsv +++ b/sub-02/ses-018/sub-02_ses-018_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/27/XX/MD5E-s4533--f3a1ed0ac8bc799649013289d9a6e061.tsv/MD5E-s4533--f3a1ed0ac8bc799649013289d9a6e061.tsv \ No newline at end of file +../../.git/annex/objects/90/VM/MD5E-s3569--cfa5897de8c015180df8f35b2fb320cd.tsv/MD5E-s3569--cfa5897de8c015180df8f35b2fb320cd.tsv \ No newline at end of file From 5a61d52ad31d8720ba7d5f61dd685f6e0252029a Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 18:02:05 -0400 Subject: [PATCH 393/463] fill IntendedFor --- ...5_ses-002_acq-sbref_dir-AP_run-01_epi.json | 94 +++---------------- ...5_ses-002_acq-sbref_dir-PA_run-01_epi.json | 88 ++--------------- ...5_ses-002_acq-sbref_dir-PA_run-02_epi.json | 88 ++--------------- ...5_ses-002_acq-sbref_dir-PA_run-03_epi.json | 88 ++--------------- ...5_ses-002_acq-sbref_dir-PA_run-04_epi.json | 88 ++--------------- ...5_ses-002_acq-sbref_dir-PA_run-05_epi.json | 88 ++--------------- ...5_ses-002_acq-sbref_dir-PA_run-06_epi.json | 88 ++--------------- ...5_ses-002_acq-sbref_dir-PA_run-07_epi.json | 88 ++--------------- 8 files changed, 62 insertions(+), 648 deletions(-) diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_epi.json index 37b28f11d..158c5f7db 100644 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997299, - -0.0733926, - 0.00289589, - 0.0704376, - 0.944482, - -0.320925 - ], + "ImageOrientationPatientDICOM": [0.997299, -0.0733926, 0.00289589, 0.0704376, 0.944482, -0.320925], "ImageOrientationText": "Tra>Cor(-18.7)>Sag(-1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,21 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-05_ses-002_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-002/func/sub-05_ses-002_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-002/func/sub-05_ses-002_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-002/func/sub-05_ses-002_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-002/func/sub-05_ses-002_task-mario3_run-05_part-mag_bold.nii.gz", + "ses-002/func/sub-05_ses-002_task-mario3_run-06_part-mag_bold.nii.gz", + "ses-002/func/sub-05_ses-002_task-mario3_run-07_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +69,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 591, - -7251, - -8832, - 449, - 14, - -302, - 16, - 26 - ], + "ShimSetting": [591, -7251, -8832, 449, 14, -302, 16, 26], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.51, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.02, 4.1175, 4.215, 4.3125, 4.41, 4.51, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_epi.json index bdbb0d013..633fafac2 100644 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997299, - -0.0733926, - 0.00289589, - 0.0704376, - 0.944482, - -0.320925 - ], + "ImageOrientationPatientDICOM": [0.997299, -0.0733926, 0.00289589, 0.0704376, 0.944482, -0.320925], "ImageOrientationText": "Tra>Cor(-18.7)>Sag(-1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-05_ses-002_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 591, - -7251, - -8832, - 449, - 14, - -302, - 16, - 26 - ], + "ShimSetting": [591, -7251, -8832, 449, 14, -302, 16, 26], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_epi.json index 0cbddc974..7b7ed02cb 100644 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997299, - -0.0733926, - 0.00289589, - 0.0704376, - 0.944482, - -0.320925 - ], + "ImageOrientationPatientDICOM": [0.997299, -0.0733926, 0.00289589, 0.0704376, 0.944482, -0.320925], "ImageOrientationText": "Tra>Cor(-18.7)>Sag(-1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-05_ses-002_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 591, - -7251, - -8832, - 449, - 14, - -302, - 16, - 26 - ], + "ShimSetting": [591, -7251, -8832, 449, 14, -302, 16, 26], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_epi.json index 05daab08f..869156174 100644 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997299, - -0.0733926, - 0.00289589, - 0.0704376, - 0.944482, - -0.320925 - ], + "ImageOrientationPatientDICOM": [0.997299, -0.0733926, 0.00289589, 0.0704376, 0.944482, -0.320925], "ImageOrientationText": "Tra>Cor(-18.7)>Sag(-1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-05_ses-002_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 591, - -7251, - -8832, - 449, - 14, - -302, - 16, - 26 - ], + "ShimSetting": [591, -7251, -8832, 449, 14, -302, 16, 26], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_epi.json index 71591a720..c960f039d 100644 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997299, - -0.0733926, - 0.00289589, - 0.0704376, - 0.944482, - -0.320925 - ], + "ImageOrientationPatientDICOM": [0.997299, -0.0733926, 0.00289589, 0.0704376, 0.944482, -0.320925], "ImageOrientationText": "Tra>Cor(-18.7)>Sag(-1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-05_ses-002_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 591, - -7251, - -8832, - 449, - 14, - -302, - 16, - 26 - ], + "ShimSetting": [591, -7251, -8832, 449, 14, -302, 16, 26], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_epi.json index 27e511648..4901a16e4 100644 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997299, - -0.0733926, - 0.00289589, - 0.0704376, - 0.944482, - -0.320925 - ], + "ImageOrientationPatientDICOM": [0.997299, -0.0733926, 0.00289589, 0.0704376, 0.944482, -0.320925], "ImageOrientationText": "Tra>Cor(-18.7)>Sag(-1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-05_ses-002_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 591, - -7251, - -8832, - 449, - 14, - -302, - 16, - 26 - ], + "ShimSetting": [591, -7251, -8832, 449, 14, -302, 16, 26], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_epi.json index 8456cfbdd..bfcd9fde9 100644 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_epi.json +++ b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-06_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997299, - -0.0733926, - 0.00289589, - 0.0704376, - 0.944482, - -0.320925 - ], + "ImageOrientationPatientDICOM": [0.997299, -0.0733926, 0.00289589, 0.0704376, 0.944482, -0.320925], "ImageOrientationText": "Tra>Cor(-18.7)>Sag(-1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-05_ses-002_task-mario3_run-06_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-06_SBRef", "SeriesNumber": 24, - "ShimSetting": [ - 591, - -7251, - -8832, - 449, - 14, - -302, - 16, - 26 - ], + "ShimSetting": [591, -7251, -8832, 449, 14, -302, 16, 26], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_epi.json b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_epi.json index 84507b25c..b4c11d8ed 100644 --- a/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_epi.json +++ b/sub-05/ses-002/fmap/sub-05_ses-002_acq-sbref_dir-PA_run-07_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997299, - -0.0733926, - 0.00289589, - 0.0704376, - 0.944482, - -0.320925 - ], + "ImageOrientationPatientDICOM": [0.997299, -0.0733926, 0.00289589, 0.0704376, 0.944482, -0.320925], "ImageOrientationText": "Tra>Cor(-18.7)>Sag(-1.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-05_ses-002_task-mario3_run-07_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-07_SBRef", "SeriesNumber": 27, - "ShimSetting": [ - 591, - -7251, - -8832, - 449, - 14, - -302, - 16, - 26 - ], + "ShimSetting": [591, -7251, -8832, 449, 14, -302, 16, 26], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 24f838b96702a7d77099deb45fd07090308da8d7 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 18:02:13 -0400 Subject: [PATCH 394/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..e1cbf3e29 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 5b0b05bc-f70b-4da2-99a8-bf371be385e4 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..38389a368 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 38389a36823e0e73c4d13ab3113eaa43198a4f88 From 0575786da5ac3a1c6f588787adac4af264d7e5d9 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 18:02:29 -0400 Subject: [PATCH 395/463] fix complex event files --- ...g_events.tsv => sub-02_ses-018_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-02_ses-018_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-02_ses-018_task-mario3_run-03_events.tsv} | 0 ...e_events.tsv => sub-02_ses-018_task-mario3_run-04_events.tsv} | 0 .../func/sub-02_ses-018_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-02_ses-018_task-mario3_run-04_part-phase_events.tsv | 1 - ...g_events.tsv => sub-02_ses-018_task-mario3_run-05_events.tsv} | 0 .../func/sub-02_ses-018_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-02_ses-018_task-mario3_run-05_part-phase_events.tsv | 1 - ...e_events.tsv => sub-02_ses-018_task-mario3_run-06_events.tsv} | 0 .../func/sub-02_ses-018_task-mario3_run-06_part-mag_events.tsv | 1 - .../func/sub-02_ses-018_task-mario3_run-06_part-phase_events.tsv | 1 - 12 files changed, 6 deletions(-) rename sub-02/ses-018/func/{sub-02_ses-018_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-018_task-mario3_run-01_events.tsv} (100%) rename sub-02/ses-018/func/{sub-02_ses-018_task-mario3_run-01_part-phase_events.tsv => sub-02_ses-018_task-mario3_run-02_events.tsv} (100%) rename sub-02/ses-018/func/{sub-02_ses-018_task-mario3_run-02_part-mag_events.tsv => sub-02_ses-018_task-mario3_run-03_events.tsv} (100%) rename sub-02/ses-018/func/{sub-02_ses-018_task-mario3_run-02_part-phase_events.tsv => sub-02_ses-018_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_part-phase_events.tsv rename sub-02/ses-018/func/{sub-02_ses-018_task-mario3_run-03_part-mag_events.tsv => sub-02_ses-018_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_part-phase_events.tsv rename sub-02/ses-018/func/{sub-02_ses-018_task-mario3_run-03_part-phase_events.tsv => sub-02_ses-018_task-mario3_run-06_events.tsv} (100%) delete mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-mag_events.tsv delete mode 120000 sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-phase_events.tsv diff --git a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_events.tsv similarity index 100% rename from sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-01_part-phase_events.tsv rename to sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_events.tsv diff --git a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_part-mag_events.tsv b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_events.tsv similarity index 100% rename from sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_part-mag_events.tsv rename to sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_events.tsv diff --git a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_part-phase_events.tsv b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_events.tsv similarity index 100% rename from sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_part-phase_events.tsv rename to sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_events.tsv diff --git a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_part-mag_events.tsv b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_part-phase_events.tsv b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_part-mag_events.tsv b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_events.tsv similarity index 100% rename from sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_part-mag_events.tsv rename to sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_events.tsv diff --git a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_part-mag_events.tsv b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_part-phase_events.tsv b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_part-phase_events.tsv b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_events.tsv similarity index 100% rename from sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_part-phase_events.tsv rename to sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_events.tsv diff --git a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-mag_events.tsv b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-phase_events.tsv b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-06_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 03fb461532fd83586c89e4191b36211d13ec94dc Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 18:03:06 -0400 Subject: [PATCH 396/463] fill IntendedFor --- ...2_ses-018_acq-sbref_dir-AP_run-01_epi.json | 93 +++---------------- ...2_ses-018_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...2_ses-018_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...2_ses-018_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...2_ses-018_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- ...2_ses-018_acq-sbref_dir-PA_run-05_epi.json | 88 ++---------------- ...2_ses-018_acq-sbref_dir-PA_run-06_epi.json | 88 ++---------------- 7 files changed, 54 insertions(+), 567 deletions(-) diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_epi.json index f78e2c6c4..e1439169d 100644 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998222, - 0.0142458, - 0.057874, - 0.0160298, - 0.871069, - -0.4909 - ], + "ImageOrientationPatientDICOM": [0.998222, 0.0142458, 0.057874, 0.0160298, 0.871069, -0.4909], "ImageOrientationText": "Tra>Cor(-29.5)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,20 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-02_ses-018_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-018/func/sub-02_ses-018_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-018/func/sub-02_ses-018_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-018/func/sub-02_ses-018_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-018/func/sub-02_ses-018_task-mario3_run-05_part-mag_bold.nii.gz", + "ses-018/func/sub-02_ses-018_task-mario3_run-06_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +68,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 618, - -7192, - -8865, - 262, - 5, - -162, - -11, - 45 - ], + "ShimSetting": [618, -7192, -8865, 262, 5, -162, -11, 45], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.51, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.02, 4.1175, 4.215, 4.3125, 4.41, 4.51, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_epi.json index 5d343b8cc..e940fbd42 100644 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998222, - 0.0142458, - 0.057874, - 0.0160298, - 0.871069, - -0.4909 - ], + "ImageOrientationPatientDICOM": [0.998222, 0.0142458, 0.057874, 0.0160298, 0.871069, -0.4909], "ImageOrientationText": "Tra>Cor(-29.5)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-02_ses-018_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 618, - -7192, - -8865, - 262, - 5, - -162, - -11, - 45 - ], + "ShimSetting": [618, -7192, -8865, 262, 5, -162, -11, 45], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_epi.json index 6b80bb9de..495187749 100644 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998222, - 0.0142458, - 0.057874, - 0.0160298, - 0.871069, - -0.4909 - ], + "ImageOrientationPatientDICOM": [0.998222, 0.0142458, 0.057874, 0.0160298, 0.871069, -0.4909], "ImageOrientationText": "Tra>Cor(-29.5)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-02_ses-018_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 618, - -7192, - -8865, - 262, - 5, - -162, - -11, - 45 - ], + "ShimSetting": [618, -7192, -8865, 262, 5, -162, -11, 45], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_epi.json index f7a6d8c17..74606a367 100644 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998222, - 0.0142458, - 0.057874, - 0.0160298, - 0.871069, - -0.4909 - ], + "ImageOrientationPatientDICOM": [0.998222, 0.0142458, 0.057874, 0.0160298, 0.871069, -0.4909], "ImageOrientationText": "Tra>Cor(-29.5)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-02_ses-018_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 618, - -7192, - -8865, - 262, - 5, - -162, - -11, - 45 - ], + "ShimSetting": [618, -7192, -8865, 262, 5, -162, -11, 45], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_epi.json index 2b0340f74..8a250edd8 100644 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998222, - 0.0142458, - 0.057874, - 0.0160298, - 0.871069, - -0.4909 - ], + "ImageOrientationPatientDICOM": [0.998222, 0.0142458, 0.057874, 0.0160298, 0.871069, -0.4909], "ImageOrientationText": "Tra>Cor(-29.5)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-02_ses-018_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 618, - -7192, - -8865, - 262, - 5, - -162, - -11, - 45 - ], + "ShimSetting": [618, -7192, -8865, 262, 5, -162, -11, 45], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_epi.json index 18e66d843..ae584ec0b 100644 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998222, - 0.0142458, - 0.057874, - 0.0160298, - 0.871069, - -0.4909 - ], + "ImageOrientationPatientDICOM": [0.998222, 0.0142458, 0.057874, 0.0160298, 0.871069, -0.4909], "ImageOrientationText": "Tra>Cor(-29.5)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-02_ses-018_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 618, - -7192, - -8865, - 262, - 5, - -162, - -11, - 45 - ], + "ShimSetting": [618, -7192, -8865, 262, 5, -162, -11, 45], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_epi.json b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_epi.json index edecbac9a..3ebd92938 100644 --- a/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_epi.json +++ b/sub-02/ses-018/fmap/sub-02_ses-018_acq-sbref_dir-PA_run-06_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998222, - 0.0142458, - 0.057874, - 0.0160298, - 0.871069, - -0.4909 - ], + "ImageOrientationPatientDICOM": [0.998222, 0.0142458, 0.057874, 0.0160298, 0.871069, -0.4909], "ImageOrientationText": "Tra>Cor(-29.5)>Sag(3.3)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-018/func/sub-02_ses-018_task-mario3_run-06_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-06_SBRef", "SeriesNumber": 24, - "ShimSetting": [ - 618, - -7192, - -8865, - 262, - 5, - -162, - -11, - 45 - ], + "ShimSetting": [618, -7192, -8865, 262, 5, -162, -11, 45], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 7d856c5ab6cdcb4377bfa20e40d954cdcdfc93e7 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 18:03:41 -0400 Subject: [PATCH 397/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-06_ses-001_acq-axial_localizer.json | 81 +++ .../sub-06_ses-001_acq-axial_localizer.nii.gz | 1 + .../sub-06_ses-001_acq-coronal_localizer.json | 81 +++ ...ub-06_ses-001_acq-coronal_localizer.nii.gz | 1 + ...sub-06_ses-001_acq-sagittal_localizer.json | 86 +++ ...b-06_ses-001_acq-sagittal_localizer.nii.gz | 1 + sub-06/ses-001/anat/sub-06_ses-001_scout.json | 542 ++++++++++++++++++ .../ses-001/anat/sub-06_ses-001_scout.nii.gz | 1 + ...1_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-001_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-01_part-mag_events.tsv | 1 + ...001_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-01_part-phase_events.tsv | 1 + ...1_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-001_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-02_part-mag_events.tsv | 1 + ...001_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-02_part-phase_events.tsv | 1 + ...1_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-001_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-03_part-mag_events.tsv | 1 + ...001_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-03_part-phase_events.tsv | 1 + ...1_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-001_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...01_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...001_task-mario3_run-04_part-mag_events.tsv | 1 + ...001_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...01_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-04_part-phase_events.tsv | 1 + ...1_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + sub-06/ses-001/sub-06_ses-001_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 79 files changed, 5409 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-06/ses-001/anat/sub-06_ses-001_acq-axial_localizer.json create mode 120000 sub-06/ses-001/anat/sub-06_ses-001_acq-axial_localizer.nii.gz create mode 100644 sub-06/ses-001/anat/sub-06_ses-001_acq-coronal_localizer.json create mode 120000 sub-06/ses-001/anat/sub-06_ses-001_acq-coronal_localizer.nii.gz create mode 100644 sub-06/ses-001/anat/sub-06_ses-001_acq-sagittal_localizer.json create mode 120000 sub-06/ses-001/anat/sub-06_ses-001_acq-sagittal_localizer.nii.gz create mode 100644 sub-06/ses-001/anat/sub-06_ses-001_scout.json create mode 120000 sub-06/ses-001/anat/sub-06_ses-001_scout.nii.gz create mode 100644 sub-06/ses-001/fmap/sub-06_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-001/fmap/sub-06_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-001/fmap/sub-06_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-001/fmap/sub-06_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_part-mag_bold.json create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_part-mag_bold.nii.gz create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_part-mag_events.tsv create mode 100644 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_part-mag_sbref.json create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_part-phase_bold.json create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_part-phase_bold.nii.gz create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_part-phase_events.tsv create mode 100644 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_part-phase_sbref.json create mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_part-phase_sbref.nii.gz create mode 120000 sub-06/ses-001/sub-06_ses-001_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 38389a368..23f071b36 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 38389a36823e0e73c4d13ab3113eaa43198a4f88 +Subproject commit 23f071b3643848018af32ab5a91a30d89e6d97fb diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..db37a3f34 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-06 41 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-06/ses-001/anat/sub-06_ses-001_acq-axial_localizer.json b/sub-06/ses-001/anat/sub-06_ses-001_acq-axial_localizer.json new file mode 100644 index 000000000..9035b0cb8 --- /dev/null +++ b/sub-06/ses-001/anat/sub-06_ses-001_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:45:14.062500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": 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"PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0309405, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 238.791 +} \ No newline at end of file diff --git a/sub-06/ses-001/anat/sub-06_ses-001_acq-axial_localizer.nii.gz b/sub-06/ses-001/anat/sub-06_ses-001_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..007d2b1ac --- /dev/null +++ b/sub-06/ses-001/anat/sub-06_ses-001_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ 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"http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999477, -0.0315803, 0.00701299, 0.031759, 0.916662, -0.398399], + "ImageOrientationText": "Tra>Cor(-23.5)>Sag(-0.4)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": 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"TxRefAmp": 238.791, + "dcmmeta_affine": [ + [-1.9989532232284546, 0.06351803988218307, -0.012306030839681625, 103.85795593261719], + [0.06316052377223969, 1.8333241939544678, -0.796826958656311, -63.629852294921875], + [0.014025970362126827, 0.7967985272407532, 1.834370493888855, -78.61614990234375], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 8d82ad8e533fc959915ae0c83dfaeaaac46b783e Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 18:05:11 -0400 Subject: [PATCH 398/463] fix fmap phase --- ...6_ses-001_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-001_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-001_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-001_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-001_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-06/ses-001/sub-06_ses-001_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-06/ses-001/fmap/{sub-06_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-06_ses-001_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-001/fmap/{sub-06_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-001_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-001/fmap/sub-06_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-001/fmap/sub-06_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-001/fmap/{sub-06_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-06_ses-001_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-001/fmap/{sub-06_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-001_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-001/fmap/{sub-06_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-06_ses-001_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-06/ses-001/fmap/{sub-06_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-06_ses-001_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-06/ses-001/fmap/{sub-06_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-06_ses-001_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-06/ses-001/fmap/{sub-06_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-06_ses-001_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-06/ses-001/fmap/{sub-06_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-06_ses-001_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-06/ses-001/fmap/{sub-06_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-06_ses-001_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-06/ses-001/fmap/{sub-06_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-06_ses-001_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-06/ses-001/fmap/{sub-06_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-06_ses-001_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-001/fmap/sub-06_ses-001_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-001/fmap/sub-06_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-001/fmap/sub-06_ses-001_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-001/fmap/sub-06_ses-001_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-001/fmap/sub-06_ses-001_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-001/fmap/sub-06_ses-001_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-001/fmap/sub-06_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 2d62be0c5..000000000 --- a/sub-06/ses-001/fmap/sub-06_ses-001_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:46:14.415000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - 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sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 501080c73..000000000 --- a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:46:3.985000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999477, - -0.0315803, - 0.00701299, - 0.031759, - 0.916662, - -0.398399 - ], - "ImageOrientationText": "Tra>Cor(-23.5)>Sag(-0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0363441, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 629, - -7256, - -8845, - 519, - 19, - -266, - -114, - -28 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 238.791, - "WipMemBlock": "48d08eec-0208-4bf4-858f-34a7a2716686||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index e6917eef5..000000000 --- a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Vz/8z/MD5E-s1112463--f0465736a7f5f89a35d1cbf65cdf2f6e.nii.gz/MD5E-s1112463--f0465736a7f5f89a35d1cbf65cdf2f6e.nii.gz \ No newline at end of file diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index be201ed99..000000000 --- a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:47:53.852500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999477, - -0.0315803, - 0.00701299, - 0.031759, - 0.916662, - -0.398399 - ], - "ImageOrientationText": "Tra>Cor(-23.5)>Sag(-0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - 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1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 238.791, - "WipMemBlock": "8215c5bf-34c2-44c9-b4f1-2a51c7aca511||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 3121a4e04..000000000 --- a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3V/Gf/MD5E-s1103494--88a7ea44b7a576d7e6dc49d276ce6438.nii.gz/MD5E-s1103494--88a7ea44b7a576d7e6dc49d276ce6438.nii.gz \ No newline at end of file diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 611ca4cac..000000000 --- a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:57:23.045000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999477, - -0.0315803, - 0.00701299, - 0.031759, - 0.916662, - -0.398399 - ], - "ImageOrientationText": "Tra>Cor(-23.5)>Sag(-0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0455723, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 629, - -7256, - -8845, - 519, - 19, - -266, - -114, - -28 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 238.791, - "WipMemBlock": "9d8fc91f-2f42-4171-9a94-500ac4eb292a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index d8c6a41d9..000000000 --- a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/K0/gV/MD5E-s1103806--63ceb0fa424d8415975d3a0baba07460.nii.gz/MD5E-s1103806--63ceb0fa424d8415975d3a0baba07460.nii.gz \ No newline at end of file diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index e6730dc2b..000000000 --- a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:06:30.845000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999477, - -0.0315803, - 0.00701299, - 0.031759, - 0.916662, - -0.398399 - ], - "ImageOrientationText": "Tra>Cor(-23.5)>Sag(-0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0455723, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 629, - -7256, - -8845, - 519, - 19, - -266, - -114, - -28 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 238.791, - "WipMemBlock": "291c731f-3031-4ad3-9118-b10ab311f5d3||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index b02a3c1bb..000000000 --- a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/2f/7k/MD5E-s1103678--522d339c410052e659a8e1ae0140603a.nii.gz/MD5E-s1103678--522d339c410052e659a8e1ae0140603a.nii.gz \ No newline at end of file diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 55a04e503..000000000 --- a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:15:4.190000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999477, - -0.0315803, - 0.00701299, - 0.031759, - 0.916662, - -0.398399 - ], - "ImageOrientationText": "Tra>Cor(-23.5)>Sag(-0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0455723, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 629, - -7256, - -8845, - 519, - 19, - -266, - -114, - -28 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 238.791, - "WipMemBlock": "a73f5e98-408d-463e-86d5-51167cb9df3e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index cdf0c8eb1..000000000 --- a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/1p/6p/MD5E-s1103654--d58bd8c3f9ec29949e753bc32244357c.nii.gz/MD5E-s1103654--d58bd8c3f9ec29949e753bc32244357c.nii.gz \ No newline at end of file diff --git a/sub-06/ses-001/sub-06_ses-001_scans.tsv b/sub-06/ses-001/sub-06_ses-001_scans.tsv index 28a3d33dd..9b23e2337 120000 --- a/sub-06/ses-001/sub-06_ses-001_scans.tsv +++ b/sub-06/ses-001/sub-06_ses-001_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/Fk/Xp/MD5E-s3289--b521e6b949b6051a272c4a4d177906ae.tsv/MD5E-s3289--b521e6b949b6051a272c4a4d177906ae.tsv \ No newline at end of file +../../.git/annex/objects/pv/QP/MD5E-s2567--474f7ae9b56139f6347ad6440213292c.tsv/MD5E-s2567--474f7ae9b56139f6347ad6440213292c.tsv \ No newline at end of file From 54880a2cd2bef53c5cc6dbd6bb0ab98679096251 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 18:05:27 -0400 Subject: [PATCH 399/463] fix complex event files --- ...g_events.tsv => sub-06_ses-001_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-06_ses-001_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-06_ses-001_task-mario3_run-03_events.tsv} | 0 .../func/sub-06_ses-001_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-06_ses-001_task-mario3_run-03_part-phase_events.tsv | 1 - ...e_events.tsv => sub-06_ses-001_task-mario3_run-04_events.tsv} | 0 .../func/sub-06_ses-001_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-06_ses-001_task-mario3_run-04_part-phase_events.tsv | 1 - 8 files changed, 4 deletions(-) rename sub-06/ses-001/func/{sub-06_ses-001_task-mario3_run-01_part-mag_events.tsv => sub-06_ses-001_task-mario3_run-01_events.tsv} (100%) rename sub-06/ses-001/func/{sub-06_ses-001_task-mario3_run-01_part-phase_events.tsv => sub-06_ses-001_task-mario3_run-02_events.tsv} (100%) rename sub-06/ses-001/func/{sub-06_ses-001_task-mario3_run-02_part-mag_events.tsv => sub-06_ses-001_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_part-phase_events.tsv rename sub-06/ses-001/func/{sub-06_ses-001_task-mario3_run-02_part-phase_events.tsv => sub-06_ses-001_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_part-phase_events.tsv diff --git a/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-01_part-mag_events.tsv b/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-01_events.tsv similarity index 100% rename from sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-01_part-mag_events.tsv rename to sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-01_events.tsv diff --git a/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-01_part-phase_events.tsv b/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-02_events.tsv similarity index 100% rename from sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-01_part-phase_events.tsv rename to sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-02_events.tsv diff --git a/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-02_part-mag_events.tsv b/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_events.tsv similarity index 100% rename from sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-02_part-mag_events.tsv rename to sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_events.tsv diff --git a/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_part-mag_events.tsv b/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_part-phase_events.tsv b/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-02_part-phase_events.tsv b/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_events.tsv similarity index 100% rename from sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-02_part-phase_events.tsv rename to sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_events.tsv diff --git a/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_part-mag_events.tsv b/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_part-phase_events.tsv b/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-001/func/sub-06_ses-001_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 3d2f4ecfcaf13ddb91de051036c90315abcf7320 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 18:05:41 -0400 Subject: [PATCH 400/463] fill IntendedFor --- ...6_ses-001_acq-sbref_dir-AP_run-01_epi.json | 91 ++----------------- ...6_ses-001_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...6_ses-001_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...6_ses-001_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...6_ses-001_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 5 files changed, 38 insertions(+), 405 deletions(-) diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_epi.json b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_epi.json index 647cad5a5..93d7e02f3 100644 --- a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999477, - -0.0315803, - 0.00701299, - 0.031759, - 0.916662, - -0.398399 - ], + "ImageOrientationPatientDICOM": [0.999477, -0.0315803, 0.00701299, 0.031759, 0.916662, -0.398399], "ImageOrientationText": "Tra>Cor(-23.5)>Sag(-0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,18 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-06_ses-001_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-001/func/sub-06_ses-001_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-001/func/sub-06_ses-001_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-001/func/sub-06_ses-001_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +66,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 629, - -7256, - -8845, - 519, - 19, - -266, - -114, - -28 - ], + "ShimSetting": [629, -7256, -8845, 519, 19, -266, -114, -28], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_epi.json b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_epi.json index eafbfe55d..cd7ca7fde 100644 --- a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999477, - -0.0315803, - 0.00701299, - 0.031759, - 0.916662, - -0.398399 - ], + "ImageOrientationPatientDICOM": [0.999477, -0.0315803, 0.00701299, 0.031759, 0.916662, -0.398399], "ImageOrientationText": "Tra>Cor(-23.5)>Sag(-0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-06_ses-001_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 629, - -7256, - -8845, - 519, - 19, - -266, - -114, - -28 - ], + "ShimSetting": [629, -7256, -8845, 519, 19, -266, -114, -28], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_epi.json b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_epi.json index 37a334577..f9e2d18cf 100644 --- a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999477, - -0.0315803, - 0.00701299, - 0.031759, - 0.916662, - -0.398399 - ], + "ImageOrientationPatientDICOM": [0.999477, -0.0315803, 0.00701299, 0.031759, 0.916662, -0.398399], "ImageOrientationText": "Tra>Cor(-23.5)>Sag(-0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-06_ses-001_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 629, - -7256, - -8845, - 519, - 19, - -266, - -114, - -28 - ], + "ShimSetting": [629, -7256, -8845, 519, 19, -266, -114, -28], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_epi.json b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_epi.json index ef570c2e7..ea6eaa8ca 100644 --- a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999477, - -0.0315803, - 0.00701299, - 0.031759, - 0.916662, - -0.398399 - ], + "ImageOrientationPatientDICOM": [0.999477, -0.0315803, 0.00701299, 0.031759, 0.916662, -0.398399], "ImageOrientationText": "Tra>Cor(-23.5)>Sag(-0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-06_ses-001_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 629, - -7256, - -8845, - 519, - 19, - -266, - -114, - -28 - ], + "ShimSetting": [629, -7256, -8845, 519, 19, -266, -114, -28], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_epi.json b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_epi.json index 7040c870a..c49ed8252 100644 --- a/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-06/ses-001/fmap/sub-06_ses-001_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999477, - -0.0315803, - 0.00701299, - 0.031759, - 0.916662, - -0.398399 - ], + "ImageOrientationPatientDICOM": [0.999477, -0.0315803, 0.00701299, 0.031759, 0.916662, -0.398399], "ImageOrientationText": "Tra>Cor(-23.5)>Sag(-0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-001/func/sub-06_ses-001_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 629, - -7256, - -8845, - 519, - 19, - -266, - -114, - -28 - ], + "ShimSetting": [629, -7256, -8845, 519, 19, -266, -114, -28], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 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/dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 70818f901eae9e63161ac213a1ac84e410a43aff From 4d1a7054a5a908b3c7b1c43b9c18c742ffeda012 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 18:08:10 -0400 Subject: [PATCH 402/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-05_ses-004_acq-axial_localizer.json | 81 +++ .../sub-05_ses-004_acq-axial_localizer.nii.gz | 1 + .../sub-05_ses-004_acq-coronal_localizer.json | 81 +++ ...ub-05_ses-004_acq-coronal_localizer.nii.gz | 1 + ...sub-05_ses-004_acq-sagittal_localizer.json | 86 +++ ...b-05_ses-004_acq-sagittal_localizer.nii.gz | 1 + sub-05/ses-004/anat/sub-05_ses-004_scout.json | 542 ++++++++++++++++++ .../ses-004/anat/sub-05_ses-004_scout.nii.gz | 1 + ...4_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-06_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-06_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 + ...-004_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...04_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...004_task-mario3_run-01_part-mag_events.tsv | 1 + ...004_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...04_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-01_part-phase_events.tsv | 1 + ...4_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-004_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...04_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...004_task-mario3_run-02_part-mag_events.tsv | 1 + ...004_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...04_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-02_part-phase_events.tsv | 1 + ...4_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-004_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...04_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...004_task-mario3_run-03_part-mag_events.tsv | 1 + ...004_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...04_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-03_part-phase_events.tsv | 1 + ...4_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-004_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...04_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...004_task-mario3_run-04_part-mag_events.tsv | 1 + ...004_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...04_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-04_part-phase_events.tsv | 1 + ...4_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-004_task-mario3_run-05_part-mag_bold.json | 172 ++++++ ...04_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...004_task-mario3_run-05_part-mag_events.tsv | 1 + ...004_task-mario3_run-05_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...04_task-mario3_run-05_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-05_part-phase_events.tsv | 1 + ...4_task-mario3_run-05_part-phase_sbref.json | 153 +++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + ...-004_task-mario3_run-06_part-mag_bold.json | 172 ++++++ ...04_task-mario3_run-06_part-mag_bold.nii.gz | 1 + ...004_task-mario3_run-06_part-mag_events.tsv | 1 + ...004_task-mario3_run-06_part-mag_sbref.json | 150 +++++ ...4_task-mario3_run-06_part-mag_sbref.nii.gz | 1 + ...04_task-mario3_run-06_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-06_part-phase_bold.nii.gz | 1 + ...4_task-mario3_run-06_part-phase_events.tsv | 1 + ...4_task-mario3_run-06_part-phase_sbref.json | 153 +++++ ...task-mario3_run-06_part-phase_sbref.nii.gz | 1 + sub-05/ses-004/sub-05_ses-004_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 107 files changed, 7333 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-05/ses-004/anat/sub-05_ses-004_acq-axial_localizer.json create mode 120000 sub-05/ses-004/anat/sub-05_ses-004_acq-axial_localizer.nii.gz create mode 100644 sub-05/ses-004/anat/sub-05_ses-004_acq-coronal_localizer.json create mode 120000 sub-05/ses-004/anat/sub-05_ses-004_acq-coronal_localizer.nii.gz create mode 100644 sub-05/ses-004/anat/sub-05_ses-004_acq-sagittal_localizer.json create mode 120000 sub-05/ses-004/anat/sub-05_ses-004_acq-sagittal_localizer.nii.gz create mode 100644 sub-05/ses-004/anat/sub-05_ses-004_scout.json create mode 120000 sub-05/ses-004/anat/sub-05_ses-004_scout.nii.gz create mode 100644 sub-05/ses-004/fmap/sub-05_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 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sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-06_part-phase_sbref.nii.gz create mode 120000 sub-05/ses-004/sub-05_ses-004_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 70818f901..b94cc4c18 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 70818f901eae9e63161ac213a1ac84e410a43aff +Subproject commit b94cc4c18f3b38862048bbfe5f41520cef40d8b6 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..da8d4ae9f --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-05 50 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-05/ses-004/anat/sub-05_ses-004_acq-axial_localizer.json b/sub-05/ses-004/anat/sub-05_ses-004_acq-axial_localizer.json new file mode 100644 index 000000000..4b062c63d --- /dev/null +++ b/sub-05/ses-004/anat/sub-05_ses-004_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:40:31.080000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + 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file diff --git a/sub-05/ses-004/anat/sub-05_ses-004_acq-coronal_localizer.json b/sub-05/ses-004/anat/sub-05_ses-004_acq-coronal_localizer.json new file mode 100644 index 000000000..f36e72af7 --- /dev/null +++ b/sub-05/ses-004/anat/sub-05_ses-004_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:40:38.070000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + 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102.88732147216797], + [0.04128409922122955, 1.850327968597412, -0.7580119371414185, -69.15214538574219], + [0.014315882697701454, 0.7578805685043335, 1.8507869243621826, -64.99454498291016], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 1c28fc48b740db895816d3492065c63f6f731ed8 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 18:09:10 -0400 Subject: [PATCH 403/463] fix fmap phase --- ...5_ses-004_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-004_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-004_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-004_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-004_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-004_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-004_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-004_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - ..._ses-004_acq-sbref_dir-PA_run-06_epi.json} | 0 ...es-004_acq-sbref_dir-PA_run-06_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 - sub-05/ses-004/sub-05_ses-004_scans.tsv | 2 +- 33 files changed, 1 insertion(+), 1250 deletions(-) rename sub-05/ses-004/fmap/{sub-05_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-05_ses-004_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-004/fmap/{sub-05_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-004_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-004/fmap/sub-05_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-004/fmap/sub-05_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-004/fmap/{sub-05_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-05_ses-004_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-004/fmap/{sub-05_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-004_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-004/fmap/{sub-05_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-05_ses-004_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-05/ses-004/fmap/{sub-05_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-05_ses-004_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-05/ses-004/fmap/{sub-05_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-05_ses-004_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-05/ses-004/fmap/{sub-05_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-05_ses-004_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-05/ses-004/fmap/{sub-05_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-05_ses-004_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-05/ses-004/fmap/{sub-05_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-05_ses-004_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-05/ses-004/fmap/{sub-05_ses-004_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-05_ses-004_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-05/ses-004/fmap/{sub-05_ses-004_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-05_ses-004_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-05/ses-004/fmap/{sub-05_ses-004_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-05_ses-004_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-05/ses-004/fmap/{sub-05_ses-004_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-05_ses-004_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz rename sub-05/ses-004/fmap/{sub-05_ses-004_acq-sbref_dir-PA_run-06_part-mag_epi.json => sub-05_ses-004_acq-sbref_dir-PA_run-06_epi.json} (100%) rename sub-05/ses-004/fmap/{sub-05_ses-004_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz => sub-05_ses-004_acq-sbref_dir-PA_run-06_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_part-phase_epi.json delete mode 120000 sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-004/fmap/sub-05_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-004/fmap/sub-05_ses-004_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-004/fmap/sub-05_ses-004_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-004/fmap/sub-05_ses-004_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-004/fmap/sub-05_ses-004_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 9187363b1..000000000 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:42:22.312500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999761, -0.020642, 0.00715794, 0.0218149, 0.925164, -0.37894], - "ImageOrientationText": "Tra>Cor(-22.3)>Sag(-0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - 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"slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["184222.312500", "184223.802500", "184225.292500"], - "ContentTime": ["184309.697000", "184309.700000", "184309.702000"], - "InstanceCreationTime": ["184309.697000", "184309.700000", "184309.702000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4786.0, 4792.0, 4790.0], - "WindowWidth": [18572.0, 18572.0, 18568.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-05/ses-004/fmap/sub-05_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 745caadf9..000000000 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/WZ/zX/MD5E-s3334054--4fd72b3a43a9e3938845a4aee97ed64d.nii.gz/MD5E-s3334054--4fd72b3a43a9e3938845a4aee97ed64d.nii.gz \ No newline at end of file diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 4da34e631..000000000 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:42:11.882500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999761, - -0.020642, - 0.00715794, - 0.0218149, - 0.925164, - -0.37894 - ], - "ImageOrientationText": 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"TotalReadoutTime": 0.0576811, - "TxRefAmp": 303.404, - "WipMemBlock": "34ecedac-6916-4ba6-a8e8-07008ac9f770||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 114d9bf6f..000000000 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/9M/kw/MD5E-s1112229--c12c9c71db1f886082669139c93e7bc2.nii.gz/MD5E-s1112229--c12c9c71db1f886082669139c93e7bc2.nii.gz \ No newline at end of file diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index c44b45195..000000000 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:44:18.907500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": 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b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 4238243a5..000000000 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Kj/0J/MD5E-s1103467--0b46c6827487cfedd5340f4d72c9ff8d.nii.gz/MD5E-s1103467--0b46c6827487cfedd5340f4d72c9ff8d.nii.gz \ No newline at end of file diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 3b1a9c527..000000000 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:55:30.425000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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-../../../.git/annex/objects/83/zK/MD5E-s1103566--c44d7bab2b57147d31a03c51369f59c7.nii.gz/MD5E-s1103566--c44d7bab2b57147d31a03c51369f59c7.nii.gz \ No newline at end of file diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index dd175183e..000000000 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:07:47.600000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999761, - -0.020642, - 0.00715794, - 0.0218149, - 0.925164, - -0.37894 - ], - "ImageOrientationText": "Tra>Cor(-22.3)>Sag(-0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0752436, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 590, - -7284, - -8820, - 368, - 38, - -385, - -52, - 86 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 303.404, - "WipMemBlock": "c3c78fd1-5ea5-406a-84a8-7abdd92ab351||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 483ce22d9..000000000 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/6f/kQ/MD5E-s1103394--4ab028c00ba2e4265b6b15987416a3ec.nii.gz/MD5E-s1103394--4ab028c00ba2e4265b6b15987416a3ec.nii.gz \ No newline at end of file diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 395d9c9f8..000000000 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:18:29.150000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999761, - -0.020642, - 0.00715794, - 0.0218149, - 0.925164, - -0.37894 - ], - "ImageOrientationText": "Tra>Cor(-22.3)>Sag(-0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0752436, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 590, - -7284, - -8820, - 368, - 38, - -385, - -52, - 86 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 303.404, - "WipMemBlock": "d5371e8f-6156-4c6d-bf5f-887effa9e8c0||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 623bed124..000000000 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/8q/m2/MD5E-s1103481--6ab72f52553dd05ebbb2aa36b8c36ce5.nii.gz/MD5E-s1103481--6ab72f52553dd05ebbb2aa36b8c36ce5.nii.gz \ No newline at end of file diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index 61cfb3dc5..000000000 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:33:57.305000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999761, - -0.020642, - 0.00715794, - 0.0218149, - 0.925164, - -0.37894 - ], - "ImageOrientationText": "Tra>Cor(-22.3)>Sag(-0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-05", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0752436, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 590, - -7284, - -8820, - 368, - 38, - -385, - -52, - 86 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 303.404, - "WipMemBlock": "f3a7d6b2-bb8f-4546-b44b-c4ba0da77cd2||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index 1b0e23936..000000000 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/GV/pg/MD5E-s1103364--2285035dfafbdb0feec4a3063c36ace5.nii.gz/MD5E-s1103364--2285035dfafbdb0feec4a3063c36ace5.nii.gz \ No newline at end of file diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_part-mag_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_epi.json similarity index 100% rename from sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_part-mag_epi.json rename to sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_epi.json diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_epi.nii.gz similarity index 100% rename from sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz rename to sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_epi.nii.gz diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_part-phase_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_part-phase_epi.json deleted file mode 100644 index e9e93d715..000000000 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:48:46.832500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999761, - -0.020642, - 0.00715794, - 0.0218149, - 0.925164, - -0.37894 - ], - "ImageOrientationText": "Tra>Cor(-22.3)>Sag(-0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-06", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0752436, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-06_SBRef", - "SeriesNumber": 24, - "ShimSetting": [ - 590, - -7284, - -8820, - 368, - 38, - -385, - -52, - 86 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 303.404, - "WipMemBlock": "5cbc00b3-eaae-426e-8115-2dd1726b31c3||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz deleted file mode 120000 index b899a83c7..000000000 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/jJ/mJ/MD5E-s1103496--c797d6db7c0cefd417b0aad52f0ad190.nii.gz/MD5E-s1103496--c797d6db7c0cefd417b0aad52f0ad190.nii.gz \ No newline at end of file diff --git a/sub-05/ses-004/sub-05_ses-004_scans.tsv b/sub-05/ses-004/sub-05_ses-004_scans.tsv index 746f879e3..91b8047b8 120000 --- a/sub-05/ses-004/sub-05_ses-004_scans.tsv +++ b/sub-05/ses-004/sub-05_ses-004_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/kk/gF/MD5E-s4533--b2508414aa760a83cb12491dd2bbcb09.tsv/MD5E-s4533--b2508414aa760a83cb12491dd2bbcb09.tsv \ No newline at end of file +../../.git/annex/objects/f6/Fj/MD5E-s3569--1807d136bdb56d96a70f29cbf0e1dc54.tsv/MD5E-s3569--1807d136bdb56d96a70f29cbf0e1dc54.tsv \ No newline at end of file From 3c2a27f4fbbb9614f0b4c5bb4fa73f93e08cd09c Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 18:09:26 -0400 Subject: [PATCH 404/463] fix complex event files --- ...g_events.tsv => sub-05_ses-004_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-05_ses-004_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-05_ses-004_task-mario3_run-03_events.tsv} | 0 ...e_events.tsv => sub-05_ses-004_task-mario3_run-04_events.tsv} | 0 .../func/sub-05_ses-004_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-05_ses-004_task-mario3_run-04_part-phase_events.tsv | 1 - ...g_events.tsv => sub-05_ses-004_task-mario3_run-05_events.tsv} | 0 .../func/sub-05_ses-004_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-05_ses-004_task-mario3_run-05_part-phase_events.tsv | 1 - ...e_events.tsv => sub-05_ses-004_task-mario3_run-06_events.tsv} | 0 .../func/sub-05_ses-004_task-mario3_run-06_part-mag_events.tsv | 1 - .../func/sub-05_ses-004_task-mario3_run-06_part-phase_events.tsv | 1 - 12 files changed, 6 deletions(-) rename sub-05/ses-004/func/{sub-05_ses-004_task-mario3_run-01_part-mag_events.tsv => sub-05_ses-004_task-mario3_run-01_events.tsv} (100%) rename sub-05/ses-004/func/{sub-05_ses-004_task-mario3_run-01_part-phase_events.tsv => sub-05_ses-004_task-mario3_run-02_events.tsv} (100%) rename sub-05/ses-004/func/{sub-05_ses-004_task-mario3_run-02_part-mag_events.tsv => sub-05_ses-004_task-mario3_run-03_events.tsv} (100%) rename sub-05/ses-004/func/{sub-05_ses-004_task-mario3_run-02_part-phase_events.tsv => sub-05_ses-004_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-04_part-phase_events.tsv rename sub-05/ses-004/func/{sub-05_ses-004_task-mario3_run-03_part-mag_events.tsv => sub-05_ses-004_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-05_part-phase_events.tsv rename sub-05/ses-004/func/{sub-05_ses-004_task-mario3_run-03_part-phase_events.tsv => sub-05_ses-004_task-mario3_run-06_events.tsv} (100%) delete mode 120000 sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-06_part-mag_events.tsv delete mode 120000 sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-06_part-phase_events.tsv diff --git a/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-01_part-mag_events.tsv b/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-01_events.tsv similarity index 100% rename from sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-01_part-mag_events.tsv rename to sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-01_events.tsv diff --git a/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-01_part-phase_events.tsv b/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-02_events.tsv similarity index 100% rename from sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-01_part-phase_events.tsv rename to sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-02_events.tsv diff --git a/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-02_part-mag_events.tsv b/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-03_events.tsv similarity index 100% rename from sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-02_part-mag_events.tsv rename to sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-03_events.tsv diff --git a/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-02_part-phase_events.tsv b/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-04_events.tsv similarity index 100% rename from sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-02_part-phase_events.tsv rename to sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-04_events.tsv diff --git a/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-04_part-mag_events.tsv b/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-04_part-phase_events.tsv b/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-03_part-mag_events.tsv b/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-05_events.tsv similarity index 100% rename from sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-03_part-mag_events.tsv rename to sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-05_events.tsv diff --git a/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-05_part-mag_events.tsv b/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-05_part-phase_events.tsv b/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-03_part-phase_events.tsv b/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-06_events.tsv similarity index 100% rename from sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-03_part-phase_events.tsv rename to sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-06_events.tsv diff --git a/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-06_part-mag_events.tsv b/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-06_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-06_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-06_part-phase_events.tsv b/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-06_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-004/func/sub-05_ses-004_task-mario3_run-06_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 7b1ca896a8f244104d47e72e1f71aa1c07cfbeff Mon Sep 17 00:00:00 2001 From: test Date: Thu, 25 May 2023 18:09:41 -0400 Subject: [PATCH 405/463] fill IntendedFor --- ...5_ses-004_acq-sbref_dir-AP_run-01_epi.json | 93 +++---------------- ...5_ses-004_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...5_ses-004_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...5_ses-004_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...5_ses-004_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- ...5_ses-004_acq-sbref_dir-PA_run-05_epi.json | 88 ++---------------- ...5_ses-004_acq-sbref_dir-PA_run-06_epi.json | 88 ++---------------- 7 files changed, 54 insertions(+), 567 deletions(-) diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_epi.json index 8d81d1abf..346bfdf0f 100644 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999761, - -0.020642, - 0.00715794, - 0.0218149, - 0.925164, - -0.37894 - ], + "ImageOrientationPatientDICOM": [0.999761, -0.020642, 0.00715794, 0.0218149, 0.925164, -0.37894], "ImageOrientationText": "Tra>Cor(-22.3)>Sag(-0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,20 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-05_ses-004_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-004/func/sub-05_ses-004_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-004/func/sub-05_ses-004_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-004/func/sub-05_ses-004_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-004/func/sub-05_ses-004_task-mario3_run-05_part-mag_bold.nii.gz", + "ses-004/func/sub-05_ses-004_task-mario3_run-06_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +68,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 590, - -7284, - -8820, - 368, - 38, - -385, - -52, - 86 - ], + "ShimSetting": [590, -7284, -8820, 368, 38, -385, -52, 86], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_epi.json index 0713f7f32..377d5fcb0 100644 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999761, - -0.020642, - 0.00715794, - 0.0218149, - 0.925164, - -0.37894 - ], + "ImageOrientationPatientDICOM": [0.999761, -0.020642, 0.00715794, 0.0218149, 0.925164, -0.37894], "ImageOrientationText": "Tra>Cor(-22.3)>Sag(-0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-05_ses-004_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 590, - -7284, - -8820, - 368, - 38, - -385, - -52, - 86 - ], + "ShimSetting": [590, -7284, -8820, 368, 38, -385, -52, 86], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-02_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-02_epi.json index ef3b7cac6..1c53c0fd9 100644 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999761, - -0.020642, - 0.00715794, - 0.0218149, - 0.925164, - -0.37894 - ], + "ImageOrientationPatientDICOM": [0.999761, -0.020642, 0.00715794, 0.0218149, 0.925164, -0.37894], "ImageOrientationText": "Tra>Cor(-22.3)>Sag(-0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-05_ses-004_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 590, - -7284, - -8820, - 368, - 38, - -385, - -52, - 86 - ], + "ShimSetting": [590, -7284, -8820, 368, 38, -385, -52, 86], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_epi.json index 47f2a4893..c5196fd13 100644 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999761, - -0.020642, - 0.00715794, - 0.0218149, - 0.925164, - -0.37894 - ], + "ImageOrientationPatientDICOM": [0.999761, -0.020642, 0.00715794, 0.0218149, 0.925164, -0.37894], "ImageOrientationText": "Tra>Cor(-22.3)>Sag(-0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-05_ses-004_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 590, - -7284, - -8820, - 368, - 38, - -385, - -52, - 86 - ], + "ShimSetting": [590, -7284, -8820, 368, 38, -385, -52, 86], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_epi.json index f83133dc7..77d41ee3c 100644 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999761, - -0.020642, - 0.00715794, - 0.0218149, - 0.925164, - -0.37894 - ], + "ImageOrientationPatientDICOM": [0.999761, -0.020642, 0.00715794, 0.0218149, 0.925164, -0.37894], "ImageOrientationText": "Tra>Cor(-22.3)>Sag(-0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-05_ses-004_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 590, - -7284, - -8820, - 368, - 38, - -385, - -52, - 86 - ], + "ShimSetting": [590, -7284, -8820, 368, 38, -385, -52, 86], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_epi.json index 148ed5282..7c0efeb2e 100644 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999761, - -0.020642, - 0.00715794, - 0.0218149, - 0.925164, - -0.37894 - ], + "ImageOrientationPatientDICOM": [0.999761, -0.020642, 0.00715794, 0.0218149, 0.925164, -0.37894], "ImageOrientationText": "Tra>Cor(-22.3)>Sag(-0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-05_ses-004_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 590, - -7284, - -8820, - 368, - 38, - -385, - -52, - 86 - ], + "ShimSetting": [590, -7284, -8820, 368, 38, -385, -52, 86], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_epi.json b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_epi.json index f4b66364a..84c0e4bf1 100644 --- a/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_epi.json +++ b/sub-05/ses-004/fmap/sub-05_ses-004_acq-sbref_dir-PA_run-06_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999761, - -0.020642, - 0.00715794, - 0.0218149, - 0.925164, - -0.37894 - ], + "ImageOrientationPatientDICOM": [0.999761, -0.020642, 0.00715794, 0.0218149, 0.925164, -0.37894], "ImageOrientationText": "Tra>Cor(-22.3)>Sag(-0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-004/func/sub-05_ses-004_task-mario3_run-06_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-06_SBRef", "SeriesNumber": 24, - "ShimSetting": [ - 590, - -7284, - -8820, - 368, - 38, - -385, - -52, - 86 - ], + "ShimSetting": [590, -7284, -8820, 368, 38, -385, -52, 86], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From f5dbd0e8e1c89a52b8814bc23ee7b840e517b20e Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 10:13:29 -0400 Subject: [PATCH 406/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..2a9afaa1b --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 2cf60bd5-f8ba-460d-ab01-2d7723d8560c diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..2c98622ac --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 2c98622acf97dfa1a4b1c6b1d2f8a6cebdc13f8b From 61954dd56defea7fa54b2b8e56a082f8e9c299f7 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 10:14:02 -0400 Subject: [PATCH 407/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-01_ses-015_acq-axial_localizer.json | 81 +++ .../sub-01_ses-015_acq-axial_localizer.nii.gz | 1 + .../sub-01_ses-015_acq-coronal_localizer.json | 81 +++ ...ub-01_ses-015_acq-coronal_localizer.nii.gz | 1 + ...sub-01_ses-015_acq-sagittal_localizer.json | 86 +++ ...b-01_ses-015_acq-sagittal_localizer.nii.gz | 1 + sub-01/ses-015/anat/sub-01_ses-015_scout.json | 542 ++++++++++++++++++ .../ses-015/anat/sub-01_ses-015_scout.nii.gz | 1 + ...5_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-015_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...15_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...k-mario3_run-01_part-mag_bold__dup-01.json | 172 ++++++ ...mario3_run-01_part-mag_bold__dup-01.nii.gz | 1 + ...015_task-mario3_run-01_part-mag_events.tsv | 1 + ...015_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...15_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...mario3_run-01_part-phase_bold__dup-01.json | 178 ++++++ ...rio3_run-01_part-phase_bold__dup-01.nii.gz | 1 + ...5_task-mario3_run-01_part-phase_events.tsv | 1 + ...5_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-mario3_run-01_sbref__part-mag_dup-01.json | 150 +++++ ...ario3_run-01_sbref__part-mag_dup-01.nii.gz | 1 + ...ario3_run-01_sbref__part-phase_dup-01.json | 153 +++++ ...io3_run-01_sbref__part-phase_dup-01.nii.gz | 1 + ...-015_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...15_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...015_task-mario3_run-02_part-mag_events.tsv | 1 + ...015_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...15_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-02_part-phase_events.tsv | 1 + ...5_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-015_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...15_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...015_task-mario3_run-03_part-mag_events.tsv | 1 + ...015_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...5_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...15_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...5_task-mario3_run-03_part-phase_events.tsv | 1 + ...5_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + sub-01/ses-015/sub-01_ses-015_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 77 files changed, 5407 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-01/ses-015/anat/sub-01_ses-015_acq-axial_localizer.json create mode 120000 sub-01/ses-015/anat/sub-01_ses-015_acq-axial_localizer.nii.gz create mode 100644 sub-01/ses-015/anat/sub-01_ses-015_acq-coronal_localizer.json create mode 120000 sub-01/ses-015/anat/sub-01_ses-015_acq-coronal_localizer.nii.gz create mode 100644 sub-01/ses-015/anat/sub-01_ses-015_acq-sagittal_localizer.json create mode 120000 sub-01/ses-015/anat/sub-01_ses-015_acq-sagittal_localizer.nii.gz create mode 100644 sub-01/ses-015/anat/sub-01_ses-015_scout.json create mode 120000 sub-01/ses-015/anat/sub-01_ses-015_scout.nii.gz create mode 100644 sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_part-mag_bold.nii.gz create mode 100644 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_part-mag_bold__dup-01.json create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_part-mag_bold__dup-01.nii.gz create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_part-phase_bold.nii.gz create mode 100644 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_part-phase_bold__dup-01.json create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_part-phase_bold__dup-01.nii.gz create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_sbref__part-mag_dup-01.json create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_sbref__part-mag_dup-01.nii.gz create mode 100644 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_sbref__part-phase_dup-01.json create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_sbref__part-phase_dup-01.nii.gz create mode 100644 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-phase_sbref.nii.gz create mode 120000 sub-01/ses-015/sub-01_ses-015_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 2c98622ac..e5c713d8e 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 2c98622acf97dfa1a4b1c6b1d2f8a6cebdc13f8b +Subproject commit e5c713d8e8fa951b70bd37eaf87b741a48447cf2 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..17ce4f7d7 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-01 45 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-01/ses-015/anat/sub-01_ses-015_acq-axial_localizer.json b/sub-01/ses-015/anat/sub-01_ses-015_acq-axial_localizer.json new file mode 100644 index 000000000..2a67998ff --- /dev/null +++ b/sub-01/ses-015/anat/sub-01_ses-015_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:23:45.200000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + 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+../../../.git/annex/objects/83/VJ/MD5E-s357440432--76e663b50d4cc92717bfd8c465c15729.nii.gz/MD5E-s357440432--76e663b50d4cc92717bfd8c465c15729.nii.gz \ No newline at end of file diff --git a/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-phase_events.tsv new file mode 120000 index 000000000..1bbdfddb5 --- /dev/null +++ b/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-phase_events.tsv @@ -0,0 +1 @@ +../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-phase_sbref.json b/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-phase_sbref.json new file mode 100644 index 000000000..d97296cf5 --- /dev/null +++ b/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-phase_sbref.json @@ -0,0 +1,153 @@ +{ + 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"75c509b6-e70f-4ded-b267-836753630ce1||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-phase_sbref.nii.gz b/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-phase_sbref.nii.gz new file mode 120000 index 000000000..4e412e36f --- /dev/null +++ b/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/k9/Qp/MD5E-s1103826--c7e3d15eaebf497522c9adf937acee64.nii.gz/MD5E-s1103826--c7e3d15eaebf497522c9adf937acee64.nii.gz \ No newline at end of file diff --git a/sub-01/ses-015/sub-01_ses-015_scans.tsv b/sub-01/ses-015/sub-01_ses-015_scans.tsv new file mode 120000 index 000000000..33fe25173 --- /dev/null +++ b/sub-01/ses-015/sub-01_ses-015_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/81/1M/MD5E-s3321--b5e872f81eab9ec4dcf92905a9ea4afe.tsv/MD5E-s3321--b5e872f81eab9ec4dcf92905a9ea4afe.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..2fb514e6e --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.997212, 0.0722078, 0.0188308, -0.0601187, 0.926881, -0.370509], + 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"ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [616, -7191, -8816, 621, 85, 13, -89, 6], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 251.672, + "dcmmeta_affine": [ + [-1.9944236278533936, -0.12023738026618958, 0.08841511607170105, 110.22505187988281], + [-0.14441557228565216, 1.8537627458572388, -0.7366868853569031, -51.403167724609375], + [0.03766167536377907, 0.7410171627998352, 1.857276201248169, -60.37505340576172], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 7dcf9372893995bc4168be21e6d9f9f3f95d60bd Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 10:14:48 -0400 Subject: [PATCH 408/463] fix fmap phase --- ...1_ses-015_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-015_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-015_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-015_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-015_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-015_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-015_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-015_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-01/ses-015/sub-01_ses-015_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-01/ses-015/fmap/{sub-01_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-01_ses-015_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-015/fmap/{sub-01_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-015_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-015/fmap/{sub-01_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-01_ses-015_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-01/ses-015/fmap/{sub-01_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-01_ses-015_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-01/ses-015/fmap/{sub-01_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-01_ses-015_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-01/ses-015/fmap/{sub-01_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-01_ses-015_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-01/ses-015/fmap/{sub-01_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-01_ses-015_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-01/ses-015/fmap/{sub-01_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-01_ses-015_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-01/ses-015/fmap/{sub-01_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-01_ses-015_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-01/ses-015/fmap/{sub-01_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-01_ses-015_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-01/ses-015/fmap/{sub-01_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-01_ses-015_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-01/ses-015/fmap/{sub-01_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-01_ses-015_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 2ca8b888c..000000000 --- a/sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:24:46.720000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 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"slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["112446.720000", "112448.210000", "112449.700000"], - "ContentTime": ["112532.116000", "112532.119000", "112532.121000"], - "InstanceCreationTime": ["112532.116000", "112532.119000", "112532.121000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4808.0, 4828.0, 4806.0], - "WindowWidth": [18620.0, 18648.0, 18622.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 1a5cc3ea4..000000000 --- a/sub-01/ses-015/fmap/sub-01_ses-015_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/v2/pj/MD5E-s3335154--f0fbf842189d11256d733980e339c14a.nii.gz/MD5E-s3335154--f0fbf842189d11256d733980e339c14a.nii.gz \ No newline at end of file diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 7a6eb4b55..000000000 --- a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:24:36.290000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997212, - 0.0722078, - 0.0188308, - -0.0601187, - 0.926881, - -0.370509 - ], - "ImageOrientationText": 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"TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.672, - "WipMemBlock": "7ad7112c-6455-425e-888c-29e6b2fd5fca||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index f358af49c..000000000 --- a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/QX/Qv/MD5E-s1112109--6e8b786ce01483a9f3952e56ef303efb.nii.gz/MD5E-s1112109--6e8b786ce01483a9f3952e56ef303efb.nii.gz \ No newline at end of file diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index bc406b7cf..000000000 --- a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:25:58.757500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997212, - 0.0722078, - 0.0188308, - -0.0601187, - 0.926881, - -0.370509 - ], - "ImageOrientationText": "Tra>Cor(-21.6)>Sag(2.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - 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"SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.672, - "WipMemBlock": "ff0ba45d-999c-42c8-8c61-af4f5da5d093||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 8ae636bc4..000000000 --- a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/PQ/q5/MD5E-s1103910--1afed6dfa07e3345a9ba5dafae95ed65.nii.gz/MD5E-s1103910--1afed6dfa07e3345a9ba5dafae95ed65.nii.gz \ No newline at end of file diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index bcf6309aa..000000000 --- a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:31:48.332500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997212, - 0.0722078, - 0.0188308, - -0.0601187, - 0.926881, - -0.370509 - ], - "ImageOrientationText": "Tra>Cor(-21.6)>Sag(2.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.048271, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 616, - -7191, - -8816, - 621, - 85, - 13, - -89, - 6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.672, - "WipMemBlock": "2ac15d0a-2dfd-440d-96f8-7ed5472663b0||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 232027d8f..000000000 --- a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/z8/9F/MD5E-s1103837--c63925f5786d368b0b8dff41613ce7e1.nii.gz/MD5E-s1103837--c63925f5786d368b0b8dff41613ce7e1.nii.gz \ No newline at end of file diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 072e6d841..000000000 --- a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:42:38.162500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997212, - 0.0722078, - 0.0188308, - -0.0601187, - 0.926881, - -0.370509 - ], - "ImageOrientationText": "Tra>Cor(-21.6)>Sag(2.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.048271, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 616, - -7191, - -8816, - 621, - 85, - 13, - -89, - 6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.672, - "WipMemBlock": "b5b03abe-f1fd-4db2-8b99-5e7097dcaca6||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index d3c1f5efb..000000000 --- a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Qw/Gx/MD5E-s1103798--2617f083d99422e9f04183ebf299f346.nii.gz/MD5E-s1103798--2617f083d99422e9f04183ebf299f346.nii.gz \ No newline at end of file diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index e79b5abb9..000000000 --- a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:53:18.977500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997212, - 0.0722078, - 0.0188308, - -0.0601187, - 0.926881, - -0.370509 - ], - "ImageOrientationText": "Tra>Cor(-21.6)>Sag(2.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.048271, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 616, - -7191, - -8816, - 621, - 85, - 13, - -89, - 6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 251.672, - "WipMemBlock": "75c509b6-e70f-4ded-b267-836753630ce1||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 4e412e36f..000000000 --- a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/k9/Qp/MD5E-s1103826--c7e3d15eaebf497522c9adf937acee64.nii.gz/MD5E-s1103826--c7e3d15eaebf497522c9adf937acee64.nii.gz \ No newline at end of file diff --git a/sub-01/ses-015/sub-01_ses-015_scans.tsv b/sub-01/ses-015/sub-01_ses-015_scans.tsv index 33fe25173..1781f47f4 120000 --- a/sub-01/ses-015/sub-01_ses-015_scans.tsv +++ b/sub-01/ses-015/sub-01_ses-015_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/81/1M/MD5E-s3321--b5e872f81eab9ec4dcf92905a9ea4afe.tsv/MD5E-s3321--b5e872f81eab9ec4dcf92905a9ea4afe.tsv \ No newline at end of file +../../.git/annex/objects/p0/0J/MD5E-s2599--212cfe6ba47a446295f735ee28372f58.tsv/MD5E-s2599--212cfe6ba47a446295f735ee28372f58.tsv \ No newline at end of file From 9b0dedb7ae138ac2fd3e417f14a88f94488bf96e Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 10:14:59 -0400 Subject: [PATCH 409/463] fix complex event files --- ...g_events.tsv => sub-01_ses-015_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-01_ses-015_task-mario3_run-02_events.tsv} | 0 .../func/sub-01_ses-015_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-01_ses-015_task-mario3_run-03_events.tsv} | 0 .../func/sub-01_ses-015_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-01_ses-015_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-01/ses-015/func/{sub-01_ses-015_task-mario3_run-01_part-mag_events.tsv => sub-01_ses-015_task-mario3_run-01_events.tsv} (100%) rename sub-01/ses-015/func/{sub-01_ses-015_task-mario3_run-01_part-phase_events.tsv => sub-01_ses-015_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-02_part-phase_events.tsv rename sub-01/ses-015/func/{sub-01_ses-015_task-mario3_run-02_part-mag_events.tsv => sub-01_ses-015_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_part-mag_events.tsv b/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_events.tsv similarity index 100% rename from sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_part-mag_events.tsv rename to sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_events.tsv diff --git a/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_part-phase_events.tsv b/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-02_events.tsv similarity index 100% rename from sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-01_part-phase_events.tsv rename to sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-02_events.tsv diff --git a/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-02_part-phase_events.tsv b/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-02_part-mag_events.tsv b/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_events.tsv similarity index 100% rename from sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-02_part-mag_events.tsv rename to sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_events.tsv diff --git a/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-mag_events.tsv b/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-phase_events.tsv b/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-015/func/sub-01_ses-015_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From e6cc902261d90f2bf23bd82e8352267f9a969844 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 10:15:12 -0400 Subject: [PATCH 410/463] fill IntendedFor --- ...1_ses-015_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...1_ses-015_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...1_ses-015_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...1_ses-015_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_epi.json b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_epi.json index 35fb1c7dd..1b92356fe 100644 --- a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997212, - 0.0722078, - 0.0188308, - -0.0601187, - 0.926881, - -0.370509 - ], + "ImageOrientationPatientDICOM": [0.997212, 0.0722078, 0.0188308, -0.0601187, 0.926881, -0.370509], "ImageOrientationText": "Tra>Cor(-21.6)>Sag(2.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-01_ses-015_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-015/func/sub-01_ses-015_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-015/func/sub-01_ses-015_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 616, - -7191, - -8816, - 621, - 85, - 13, - -89, - 6 - ], + "ShimSetting": [616, -7191, -8816, 621, 85, 13, -89, 6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_epi.json b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_epi.json index b1f5eb881..7d0fe7a65 100644 --- a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997212, - 0.0722078, - 0.0188308, - -0.0601187, - 0.926881, - -0.370509 - ], + "ImageOrientationPatientDICOM": [0.997212, 0.0722078, 0.0188308, -0.0601187, 0.926881, -0.370509], "ImageOrientationText": "Tra>Cor(-21.6)>Sag(2.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-01_ses-015_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 616, - -7191, - -8816, - 621, - 85, - 13, - -89, - 6 - ], + "ShimSetting": [616, -7191, -8816, 621, 85, 13, -89, 6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.4875, 0.5875, 0.685, 0.7825, 0.88, 0.9775, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.485, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_epi.json b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_epi.json index f48095eac..baae2c44b 100644 --- a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997212, - 0.0722078, - 0.0188308, - -0.0601187, - 0.926881, - -0.370509 - ], + "ImageOrientationPatientDICOM": [0.997212, 0.0722078, 0.0188308, -0.0601187, 0.926881, -0.370509], "ImageOrientationText": "Tra>Cor(-21.6)>Sag(2.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-01_ses-015_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 616, - -7191, - -8816, - 621, - 85, - 13, - -89, - 6 - ], + "ShimSetting": [616, -7191, -8816, 621, 85, 13, -89, 6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_epi.json b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_epi.json index 5efbb5a5d..bb879f542 100644 --- a/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-01/ses-015/fmap/sub-01_ses-015_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.997212, - 0.0722078, - 0.0188308, - -0.0601187, - 0.926881, - -0.370509 - ], + "ImageOrientationPatientDICOM": [0.997212, 0.0722078, 0.0188308, -0.0601187, 0.926881, -0.370509], "ImageOrientationText": "Tra>Cor(-21.6)>Sag(2.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-015/func/sub-01_ses-015_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 616, - -7191, - -8816, - 621, - 85, - 13, - -89, - 6 - ], + "ShimSetting": [616, -7191, -8816, 621, 85, 13, -89, 6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 001c436e6ac0bb83464bd76f9e6e371e583ded5c Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:01:30 -0400 Subject: [PATCH 411/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..b2e51334a --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = d9ec4151-6293-45e9-91c9-d447b7951ce2 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..0f40f00d8 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 0f40f00d89862afd66d7ce046b7a61ec8cb2669a From f587de2d8835aa86ef1e79c23b5f385220379647 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:01:58 -0400 Subject: [PATCH 412/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-02_ses-013_acq-axial_localizer.json | 81 +++ .../sub-02_ses-013_acq-axial_localizer.nii.gz | 1 + .../sub-02_ses-013_acq-coronal_localizer.json | 81 +++ ...ub-02_ses-013_acq-coronal_localizer.nii.gz | 1 + ...sub-02_ses-013_acq-sagittal_localizer.json | 86 +++ ...b-02_ses-013_acq-sagittal_localizer.nii.gz | 1 + sub-02/ses-013/anat/sub-02_ses-013_scout.json | 542 ++++++++++++++++++ .../ses-013/anat/sub-02_ses-013_scout.nii.gz | 1 + ...3_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ...-013_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...13_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...k-mario3_run-01_part-mag_bold__dup-01.json | 172 ++++++ ...mario3_run-01_part-mag_bold__dup-01.nii.gz | 1 + ...k-mario3_run-01_part-mag_bold__dup-02.json | 172 ++++++ ...mario3_run-01_part-mag_bold__dup-02.nii.gz | 1 + ...k-mario3_run-01_part-mag_bold__dup-03.json | 172 ++++++ ...mario3_run-01_part-mag_bold__dup-03.nii.gz | 1 + ...k-mario3_run-01_part-mag_bold__dup-04.json | 172 ++++++ ...mario3_run-01_part-mag_bold__dup-04.nii.gz | 1 + ...013_task-mario3_run-01_part-mag_events.tsv | 1 + ...013_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...3_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...13_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...mario3_run-01_part-phase_bold__dup-01.json | 178 ++++++ ...rio3_run-01_part-phase_bold__dup-01.nii.gz | 1 + ...mario3_run-01_part-phase_bold__dup-02.json | 178 ++++++ ...rio3_run-01_part-phase_bold__dup-02.nii.gz | 1 + ...mario3_run-01_part-phase_bold__dup-03.json | 178 ++++++ ...rio3_run-01_part-phase_bold__dup-03.nii.gz | 1 + ...mario3_run-01_part-phase_bold__dup-04.json | 178 ++++++ ...rio3_run-01_part-phase_bold__dup-04.nii.gz | 1 + ...3_task-mario3_run-01_part-phase_events.tsv | 1 + ...3_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-mario3_run-01_sbref__part-mag_dup-01.json | 150 +++++ ...ario3_run-01_sbref__part-mag_dup-01.nii.gz | 1 + ...-mario3_run-01_sbref__part-mag_dup-02.json | 150 +++++ ...ario3_run-01_sbref__part-mag_dup-02.nii.gz | 1 + ...-mario3_run-01_sbref__part-mag_dup-03.json | 150 +++++ ...ario3_run-01_sbref__part-mag_dup-03.nii.gz | 1 + ...-mario3_run-01_sbref__part-mag_dup-04.json | 150 +++++ ...ario3_run-01_sbref__part-mag_dup-04.nii.gz | 1 + ...ario3_run-01_sbref__part-phase_dup-01.json | 153 +++++ ...io3_run-01_sbref__part-phase_dup-01.nii.gz | 1 + ...ario3_run-01_sbref__part-phase_dup-02.json | 153 +++++ ...io3_run-01_sbref__part-phase_dup-02.nii.gz | 1 + ...ario3_run-01_sbref__part-phase_dup-03.json | 153 +++++ ...io3_run-01_sbref__part-phase_dup-03.nii.gz | 1 + ...ario3_run-01_sbref__part-phase_dup-04.json | 153 +++++ ...io3_run-01_sbref__part-phase_dup-04.nii.gz | 1 + sub-02/ses-013/sub-02_ses-013_scans.tsv | 1 + task-mario3_bold.json | 81 +++ 85 files changed, 6369 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-02/ses-013/anat/sub-02_ses-013_acq-axial_localizer.json create mode 120000 sub-02/ses-013/anat/sub-02_ses-013_acq-axial_localizer.nii.gz create mode 100644 sub-02/ses-013/anat/sub-02_ses-013_acq-coronal_localizer.json create mode 120000 sub-02/ses-013/anat/sub-02_ses-013_acq-coronal_localizer.nii.gz create mode 100644 sub-02/ses-013/anat/sub-02_ses-013_acq-sagittal_localizer.json create mode 120000 sub-02/ses-013/anat/sub-02_ses-013_acq-sagittal_localizer.nii.gz create mode 100644 sub-02/ses-013/anat/sub-02_ses-013_scout.json create mode 120000 sub-02/ses-013/anat/sub-02_ses-013_scout.nii.gz create mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_part-mag_epi.json create mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz create mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_part-phase_epi.json create mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-mag_bold.nii.gz create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-mag_bold__dup-01.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-mag_bold__dup-01.nii.gz create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-mag_bold__dup-02.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-mag_bold__dup-02.nii.gz create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-mag_bold__dup-03.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-mag_bold__dup-03.nii.gz create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-mag_bold__dup-04.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-mag_bold__dup-04.nii.gz create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-phase_bold.nii.gz create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-phase_bold__dup-01.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-phase_bold__dup-01.nii.gz create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-phase_bold__dup-02.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-phase_bold__dup-02.nii.gz create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-phase_bold__dup-03.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-phase_bold__dup-03.nii.gz create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-phase_bold__dup-04.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-phase_bold__dup-04.nii.gz create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-mag_dup-01.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-mag_dup-01.nii.gz create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-mag_dup-02.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-mag_dup-02.nii.gz create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-mag_dup-03.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-mag_dup-03.nii.gz create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-mag_dup-04.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-mag_dup-04.nii.gz create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-phase_dup-01.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-phase_dup-01.nii.gz create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-phase_dup-02.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-phase_dup-02.nii.gz create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-phase_dup-03.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-phase_dup-03.nii.gz create mode 100644 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-phase_dup-04.json create mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-phase_dup-04.nii.gz create mode 120000 sub-02/ses-013/sub-02_ses-013_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 0f40f00d8..cb073cd09 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 0f40f00d89862afd66d7ce046b7a61ec8cb2669a +Subproject commit cb073cd09c7152ad166e6a1044c397b530faa730 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..83ada7a9d --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-02 51 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-02/ses-013/anat/sub-02_ses-013_acq-axial_localizer.json b/sub-02/ses-013/anat/sub-02_ses-013_acq-axial_localizer.json new file mode 100644 index 000000000..877b73d1e --- /dev/null +++ b/sub-02/ses-013/anat/sub-02_ses-013_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:35:45.040000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.0480244, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 299.478 +} \ No newline at end of file diff --git a/sub-02/ses-013/anat/sub-02_ses-013_acq-axial_localizer.nii.gz b/sub-02/ses-013/anat/sub-02_ses-013_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..b4349214f --- /dev/null +++ b/sub-02/ses-013/anat/sub-02_ses-013_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Xv/qq/MD5E-s184476--a7c2cb2d6bf180b9c52eecc787540f13.nii.gz/MD5E-s184476--a7c2cb2d6bf180b9c52eecc787540f13.nii.gz \ No newline at end of file diff --git a/sub-02/ses-013/anat/sub-02_ses-013_acq-coronal_localizer.json b/sub-02/ses-013/anat/sub-02_ses-013_acq-coronal_localizer.json new file mode 100644 index 000000000..517964053 --- /dev/null +++ b/sub-02/ses-013/anat/sub-02_ses-013_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": 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newline at end of file diff --git a/sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-phase_dup-04.nii.gz b/sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-phase_dup-04.nii.gz new file mode 120000 index 000000000..e84fbc82e --- /dev/null +++ b/sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_sbref__part-phase_dup-04.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/mW/9j/MD5E-s1103291--c8749452f09b8e308c9e48e0b9960e96.nii.gz/MD5E-s1103291--c8749452f09b8e308c9e48e0b9960e96.nii.gz \ No newline at end of file diff --git a/sub-02/ses-013/sub-02_ses-013_scans.tsv b/sub-02/ses-013/sub-02_ses-013_scans.tsv new file mode 120000 index 000000000..73ff3c5a6 --- /dev/null +++ b/sub-02/ses-013/sub-02_ses-013_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/X4/q6/MD5E-s4039--76bfb43c41cb4f4a45218305e66ad486.tsv/MD5E-s4039--76bfb43c41cb4f4a45218305e66ad486.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..d571e7600 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "11:51:4.612500", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999267, -0.00206304, 0.038232, 0.0223275, 0.842582, -0.538105], + "ImageOrientationText": "Tra>Cor(-32.6)>Sag(1.8)", + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "func_task-mario3_run-01", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0707352, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "SeriesDescription": "func_task-mario3_run-01", + "ShimSetting": [611, -7191, -8859, 250, 60, -232, -46, 42], + "SliceThickness": 2, + "SliceTiming": [0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.08, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875, 0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.08, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875, 0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.08, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875, 0, 0.785, 0.1, 0.8825, 0.1975, 0.98, 0.295, 1.08, 0.3925, 1.1775, 0.49, 1.275, 0.59, 1.3725, 0.6875], + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 299.478, + "WipMemBlock": "ce240cf9-2ec0-4571-bc7d-97fb025c20d6||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", + "dcmmeta_affine": [ + [-1.9985334873199463, 0.044654980301856995, 0.06220702454447746, 103.44538879394531], + [0.0041260793805122375, 1.6851645708084106, -1.0771273374557495, -48.16771697998047], + [0.07646408677101135, 1.0762091875076294, 1.6840211153030396, -97.091552734375], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_shape": [104, 104, 60, 386], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 91a06dd1aeb9f8026d9260e0576dd44de20b1839 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:02:44 -0400 Subject: [PATCH 413/463] fix fmap phase --- ...2_ses-013_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-013_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-013_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-013_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-013_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-013_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-013_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-013_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-013_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-013_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-013_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-013_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-013_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-013_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - sub-02/ses-013/sub-02_ses-013_scans.tsv | 2 +- 29 files changed, 1 insertion(+), 1097 deletions(-) rename sub-02/ses-013/fmap/{sub-02_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-02_ses-013_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-013/fmap/{sub-02_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-013_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-013/fmap/{sub-02_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-02_ses-013_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-02/ses-013/fmap/{sub-02_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-02_ses-013_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-02/ses-013/fmap/{sub-02_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-02_ses-013_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-02/ses-013/fmap/{sub-02_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-02_ses-013_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-02/ses-013/fmap/{sub-02_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-02_ses-013_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-02/ses-013/fmap/{sub-02_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-02_ses-013_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-02/ses-013/fmap/{sub-02_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-02_ses-013_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-02/ses-013/fmap/{sub-02_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-02_ses-013_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-02/ses-013/fmap/{sub-02_ses-013_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-02_ses-013_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-02/ses-013/fmap/{sub-02_ses-013_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-02_ses-013_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-02/ses-013/fmap/{sub-02_ses-013_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-02_ses-013_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-02/ses-013/fmap/{sub-02_ses-013_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-02_ses-013_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 155079f9e..000000000 --- a/sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:36:45.967500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999267, -0.00206304, 0.038232, 0.0223275, 0.842582, -0.538105], - "ImageOrientationText": "Tra>Cor(-32.6)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0564116, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [611, 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-52.593210295112, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000344855, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "113457.280000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["113645.967500", "113647.457500", "113648.947500"], - "ContentTime": ["113732.637000", "113732.639000", "113732.656000"], - "InstanceCreationTime": ["113732.637000", "113732.639000", "113732.656000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4716.0, 4720.0, 4724.0], - "WindowWidth": [18508.0, 18508.0, 18496.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 715da1699..000000000 --- a/sub-02/ses-013/fmap/sub-02_ses-013_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/g7/kk/MD5E-s3333252--9c3fb6a78034d9755517dd58cdb190c2.nii.gz/MD5E-s3333252--9c3fb6a78034d9755517dd58cdb190c2.nii.gz \ No newline at end of file diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index eaf844904..000000000 --- a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:36:35.537500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999267, - -0.00206304, - 0.038232, - 0.0223275, - 0.842582, - -0.538105 - ], - "ImageOrientationText": "Tra>Cor(-32.6)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0564116, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 611, - -7191, - -8859, - 250, - 60, - -232, - -46, - 42 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 299.478, - "WipMemBlock": "85c93c35-31e6-491d-b3eb-47dff541dd05||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index ea776ba1c..000000000 --- a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/25/wW/MD5E-s1112130--7aa1c70d1edf73147f145ddc1bf78eff.nii.gz/MD5E-s1112130--7aa1c70d1edf73147f145ddc1bf78eff.nii.gz \ No newline at end of file diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 5c7c7a584..000000000 --- a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:38:19.530000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999267, - -0.00206304, - 0.038232, - 0.0223275, - 0.842582, - -0.538105 - ], - "ImageOrientationText": "Tra>Cor(-32.6)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0707352, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 611, - -7191, - -8859, - 250, - 60, - -232, - -46, - 42 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 299.478, - "WipMemBlock": "f32ff805-2c82-4451-b0cf-6bc66397226f||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 91fbe386a..000000000 --- a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/wv/Xj/MD5E-s1103232--cb38720d97dd2a594f56087e1887c42c.nii.gz/MD5E-s1103232--cb38720d97dd2a594f56087e1887c42c.nii.gz \ No newline at end of file diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 5c1746107..000000000 --- a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:39:52.427500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999267, - -0.00206304, - 0.038232, - 0.0223275, - 0.842582, - -0.538105 - ], - "ImageOrientationText": "Tra>Cor(-32.6)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0707352, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 611, - -7191, - -8859, - 250, - 60, - -232, - -46, - 42 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 299.478, - "WipMemBlock": "1e6add5a-4d01-46e9-a565-dc0fecd8779c||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 89308ea70..000000000 --- a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/1p/jp/MD5E-s1103443--6f17a78c0f10338ccc73da6def3ac5a5.nii.gz/MD5E-s1103443--6f17a78c0f10338ccc73da6def3ac5a5.nii.gz \ No newline at end of file diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index d02fed1c9..000000000 --- a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:41:59.802500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999267, - -0.00206304, - 0.038232, - 0.0223275, - 0.842582, - -0.538105 - ], - "ImageOrientationText": "Tra>Cor(-32.6)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0707352, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 611, - -7191, - -8859, - 250, - 60, - -232, - -46, - 42 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 299.478, - "WipMemBlock": "4101f06f-c240-4eaa-b309-ae3c6b938373||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 333fccb82..000000000 --- a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/mq/Gg/MD5E-s1103422--02d34a9f1cfa1bacb3bfc971fc15ce2d.nii.gz/MD5E-s1103422--02d34a9f1cfa1bacb3bfc971fc15ce2d.nii.gz \ No newline at end of file diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 3e5b5a388..000000000 --- a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:47:35.247500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999267, - -0.00206304, - 0.038232, - 0.0223275, - 0.842582, - -0.538105 - ], - "ImageOrientationText": "Tra>Cor(-32.6)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0707352, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 611, - -7191, - -8859, - 250, - 60, - -232, - -46, - 42 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 299.478, - "WipMemBlock": "e9a14501-77a8-4958-b6ec-3ce74b7a6e0d||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index e84fbc82e..000000000 --- a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/mW/9j/MD5E-s1103291--c8749452f09b8e308c9e48e0b9960e96.nii.gz/MD5E-s1103291--c8749452f09b8e308c9e48e0b9960e96.nii.gz \ No newline at end of file diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index fc9314e8e..000000000 --- a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:50:54.182500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999267, - -0.00206304, - 0.038232, - 0.0223275, - 0.842582, - -0.538105 - ], - "ImageOrientationText": "Tra>Cor(-32.6)>Sag(1.8)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0707352, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 611, - -7191, - -8859, - 250, - 60, - -232, - -46, - 42 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 299.478, - "WipMemBlock": "ce240cf9-2ec0-4571-bc7d-97fb025c20d6||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index 7944ac7bb..000000000 --- a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/M9/zK/MD5E-s1103300--5c3935c1eb6c7cc8d12e5dade437f3be.nii.gz/MD5E-s1103300--5c3935c1eb6c7cc8d12e5dade437f3be.nii.gz \ No newline at end of file diff --git a/sub-02/ses-013/sub-02_ses-013_scans.tsv b/sub-02/ses-013/sub-02_ses-013_scans.tsv index 73ff3c5a6..aed414d7c 120000 --- a/sub-02/ses-013/sub-02_ses-013_scans.tsv +++ b/sub-02/ses-013/sub-02_ses-013_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/X4/q6/MD5E-s4039--76bfb43c41cb4f4a45218305e66ad486.tsv/MD5E-s4039--76bfb43c41cb4f4a45218305e66ad486.tsv \ No newline at end of file +../../.git/annex/objects/Q3/kv/MD5E-s3196--6d875694e2f2ec32955564df18b47c89.tsv/MD5E-s3196--6d875694e2f2ec32955564df18b47c89.tsv \ No newline at end of file From cd6ee4c040298de118daff3efc53db2642c52ba0 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:02:54 -0400 Subject: [PATCH 414/463] fix complex event files --- ...g_events.tsv => sub-02_ses-013_task-mario3_run-01_events.tsv} | 0 .../func/sub-02_ses-013_task-mario3_run-01_part-phase_events.tsv | 1 - 2 files changed, 1 deletion(-) rename sub-02/ses-013/func/{sub-02_ses-013_task-mario3_run-01_part-mag_events.tsv => sub-02_ses-013_task-mario3_run-01_events.tsv} (100%) delete mode 120000 sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-phase_events.tsv diff --git a/sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-mag_events.tsv b/sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_events.tsv similarity index 100% rename from sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-mag_events.tsv rename to sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_events.tsv diff --git a/sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-phase_events.tsv b/sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-02/ses-013/func/sub-02_ses-013_task-mario3_run-01_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From c37e1a4ea766154d5609cc4b366a3e4f5d787639 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:03:06 -0400 Subject: [PATCH 415/463] fill IntendedFor --- ...2_ses-013_acq-sbref_dir-AP_run-01_epi.json | 88 ++----------------- ...2_ses-013_acq-sbref_dir-PA_run-05_epi.json | 88 ++----------------- 2 files changed, 14 insertions(+), 162 deletions(-) diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_epi.json b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_epi.json index e3d4b4056..a0f690438 100644 --- a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999267, - -0.00206304, - 0.038232, - 0.0223275, - 0.842582, - -0.538105 - ], + "ImageOrientationPatientDICOM": [0.999267, -0.00206304, 0.038232, 0.0223275, 0.842582, -0.538105], "ImageOrientationText": "Tra>Cor(-32.6)>Sag(1.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-013/func/sub-02_ses-013_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 611, - -7191, - -8859, - 250, - 60, - -232, - -46, - 42 - ], + "ShimSetting": [611, -7191, -8859, 250, 60, -232, -46, 42], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_epi.json b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_epi.json index 273016a82..13ae7fdb9 100644 --- a/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-02/ses-013/fmap/sub-02_ses-013_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999267, - -0.00206304, - 0.038232, - 0.0223275, - 0.842582, - -0.538105 - ], + "ImageOrientationPatientDICOM": [0.999267, -0.00206304, 0.038232, 0.0223275, 0.842582, -0.538105], "ImageOrientationText": "Tra>Cor(-32.6)>Sag(1.8)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-013/func/sub-02_ses-013_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 611, - -7191, - -8859, - 250, - 60, - -232, - -46, - 42 - ], + "ShimSetting": [611, -7191, -8859, 250, 60, -232, -46, 42], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From a10cbe0856e920e089adc0985072d28fdf19aad1 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:18:18 -0400 Subject: [PATCH 416/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..4a993a5c7 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 6dcddef9-86d7-4b94-85be-b105968dc3a0 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..aaac45b44 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit aaac45b44d6c5f48efd1c1c0c157112060839af3 From f9bf4744189fe91c133fa06562962320e2577c48 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:18:26 -0400 Subject: [PATCH 417/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..6ca6a78ed --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 4e034d00-5ef4-4bf6-8f87-e05470d38b08 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..31f495c65 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 31f495c656d5d4a2e4b410926cedf791004bd4e1 From ca0e22e6bc6b78007bfc2d6ccf26748d86b675a4 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:18:50 -0400 Subject: [PATCH 418/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-03_ses-006_acq-axial_localizer.json | 81 +++ .../sub-03_ses-006_acq-axial_localizer.nii.gz | 1 + .../sub-03_ses-006_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-006_acq-coronal_localizer.nii.gz | 1 + ...sub-03_ses-006_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-006_acq-sagittal_localizer.nii.gz | 1 + sub-03/ses-006/anat/sub-03_ses-006_scout.json | 542 ++++++++++++++++++ .../ses-006/anat/sub-03_ses-006_scout.nii.gz | 1 + ...6_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-006_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...06_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...006_task-mario3_run-01_part-mag_events.tsv | 1 + ...006_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-01_part-phase_events.tsv | 1 + ...6_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-006_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...06_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...006_task-mario3_run-02_part-mag_events.tsv | 1 + ...006_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...6_task-mario3_run-02_part-phase_events.tsv | 1 + ...6_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-006_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...06_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...k-mario3_run-03_part-mag_bold__dup-01.json | 172 ++++++ ...mario3_run-03_part-mag_bold__dup-01.nii.gz | 1 + ...006_task-mario3_run-03_part-mag_events.tsv | 1 + ...006_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...6_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...06_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...mario3_run-03_part-phase_bold__dup-01.json | 178 ++++++ ...rio3_run-03_part-phase_bold__dup-01.nii.gz | 1 + ...6_task-mario3_run-03_part-phase_events.tsv | 1 + ...6_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-mario3_run-03_sbref__part-mag_dup-01.json | 150 +++++ ...ario3_run-03_sbref__part-mag_dup-01.nii.gz | 1 + ...ario3_run-03_sbref__part-phase_dup-01.json | 153 +++++ ...io3_run-03_sbref__part-phase_dup-01.nii.gz | 1 + sub-03/ses-006/sub-03_ses-006_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 77 files changed, 5407 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-006/anat/sub-03_ses-006_acq-axial_localizer.json create mode 120000 sub-03/ses-006/anat/sub-03_ses-006_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-006/anat/sub-03_ses-006_acq-coronal_localizer.json create mode 120000 sub-03/ses-006/anat/sub-03_ses-006_acq-coronal_localizer.nii.gz create mode 100644 sub-03/ses-006/anat/sub-03_ses-006_acq-sagittal_localizer.json create mode 120000 sub-03/ses-006/anat/sub-03_ses-006_acq-sagittal_localizer.nii.gz create mode 100644 sub-03/ses-006/anat/sub-03_ses-006_scout.json create mode 120000 sub-03/ses-006/anat/sub-03_ses-006_scout.nii.gz create mode 100644 sub-03/ses-006/fmap/sub-03_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-006/fmap/sub-03_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-006/fmap/sub-03_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-006/fmap/sub-03_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 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sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-03_sbref__part-mag_dup-01.nii.gz create mode 100644 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-03_sbref__part-phase_dup-01.json create mode 120000 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-03_sbref__part-phase_dup-01.nii.gz create mode 120000 sub-03/ses-006/sub-03_ses-006_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index aaac45b44..aea509ee5 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit aaac45b44d6c5f48efd1c1c0c157112060839af3 +Subproject commit aea509ee5cdcb614a3e5f7d794e93099e4d0d74f diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-03/ses-006/anat/sub-03_ses-006_acq-axial_localizer.json b/sub-03/ses-006/anat/sub-03_ses-006_acq-axial_localizer.json new file mode 100644 index 000000000..bc4b968f0 --- /dev/null +++ b/sub-03/ses-006/anat/sub-03_ses-006_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "13:53:46.055000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + 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-0,0 +1 @@ +../../../.git/annex/objects/4K/MZ/MD5E-s165101--915af22fc278df3850e3427741b39892.nii.gz/MD5E-s165101--915af22fc278df3850e3427741b39892.nii.gz \ No newline at end of file diff --git a/sub-03/ses-006/anat/sub-03_ses-006_acq-coronal_localizer.json b/sub-03/ses-006/anat/sub-03_ses-006_acq-coronal_localizer.json new file mode 100644 index 000000000..0b78b3700 --- /dev/null +++ b/sub-03/ses-006/anat/sub-03_ses-006_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "13:53:53.045000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 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a/sub-03/ses-006/anat/sub-03_ses-006_acq-sagittal_localizer.json b/sub-03/ses-006/anat/sub-03_ses-006_acq-sagittal_localizer.json new file mode 100644 index 000000000..8384ebc41 --- /dev/null +++ b/sub-03/ses-006/anat/sub-03_ses-006_acq-sagittal_localizer.json @@ -0,0 +1,86 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "13:53:39.065000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 0, + 1, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Sag", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.26, + 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-59.30125427246094], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From e9a6d6cf65b47ea61661dce31ad41035a06e3483 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:18:59 -0400 Subject: [PATCH 419/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-06_ses-011_acq-axial_localizer.json | 81 +++ .../sub-06_ses-011_acq-axial_localizer.nii.gz | 1 + .../sub-06_ses-011_acq-coronal_localizer.json | 81 +++ ...ub-06_ses-011_acq-coronal_localizer.nii.gz | 1 + ...sub-06_ses-011_acq-sagittal_localizer.json | 86 +++ ...b-06_ses-011_acq-sagittal_localizer.nii.gz | 1 + sub-06/ses-011/anat/sub-06_ses-011_scout.json | 542 ++++++++++++++++++ .../ses-011/anat/sub-06_ses-011_scout.nii.gz | 1 + ...1_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-011_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...11_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...011_task-mario3_run-01_part-mag_events.tsv | 1 + ...011_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...11_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-01_part-phase_events.tsv | 1 + ...1_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-011_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...11_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...011_task-mario3_run-02_part-mag_events.tsv | 1 + ...011_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...11_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-02_part-phase_events.tsv | 1 + ...1_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-011_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...11_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...011_task-mario3_run-03_part-mag_events.tsv | 1 + ...011_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...1_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...11_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...1_task-mario3_run-03_part-phase_events.tsv | 1 + ...1_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-mario3_run-03_sbref__part-mag_dup-01.json | 150 +++++ ...ario3_run-03_sbref__part-mag_dup-01.nii.gz | 1 + ...ario3_run-03_sbref__part-phase_dup-01.json | 153 +++++ ...io3_run-03_sbref__part-phase_dup-01.nii.gz | 1 + sub-06/ses-011/sub-06_ses-011_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 73 files changed, 5055 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-06/ses-011/anat/sub-06_ses-011_acq-axial_localizer.json create mode 120000 sub-06/ses-011/anat/sub-06_ses-011_acq-axial_localizer.nii.gz create mode 100644 sub-06/ses-011/anat/sub-06_ses-011_acq-coronal_localizer.json create mode 120000 sub-06/ses-011/anat/sub-06_ses-011_acq-coronal_localizer.nii.gz create mode 100644 sub-06/ses-011/anat/sub-06_ses-011_acq-sagittal_localizer.json create mode 120000 sub-06/ses-011/anat/sub-06_ses-011_acq-sagittal_localizer.nii.gz create mode 100644 sub-06/ses-011/anat/sub-06_ses-011_scout.json create mode 120000 sub-06/ses-011/anat/sub-06_ses-011_scout.nii.gz create mode 100644 sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_part-mag_bold.nii.gz create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_part-phase_bold.nii.gz create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_part-phase_events.tsv create mode 100644 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_part-phase_sbref.json create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_sbref__part-mag_dup-01.json create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_sbref__part-mag_dup-01.nii.gz create mode 100644 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_sbref__part-phase_dup-01.json create mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_sbref__part-phase_dup-01.nii.gz create mode 120000 sub-06/ses-011/sub-06_ses-011_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 31f495c65..e833234da 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 31f495c656d5d4a2e4b410926cedf791004bd4e1 +Subproject commit e833234da73df692133165c6c0e912eb8d181837 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..db37a3f34 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-06 41 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-06/ses-011/anat/sub-06_ses-011_acq-axial_localizer.json b/sub-06/ses-011/anat/sub-06_ses-011_acq-axial_localizer.json new file mode 100644 index 000000000..7ed3d8cf8 --- /dev/null +++ b/sub-06/ses-011/anat/sub-06_ses-011_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:44:7.067500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 1, + 0 + ], + "ImageOrientationText": "Tra", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "NumberOfAverages": 2, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 91, + "PhaseEncodingDirection": "j-", + "PhaseEncodingSteps": 233, + "PhaseResolution": 0.91, + "PixelBandwidth": 320, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "localizer", + "PulseSequenceDetails": "%SiemensSeq%\\gre", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 512, + "RepetitionTime": 0.0075, + "SAR": 0.027379, + "ScanningSequence": "GR", + "SequenceName": "*fl2d1", + "SequenceVariant": "SP\\OSP", + "SeriesDescription": "localizer", + "SeriesNumber": 5, + "ShimSetting": [ + 621, + -7191, + -9126, + 52, + 33, + -14, + -34, + -17 + ], + "SliceThickness": 7, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 8.4, + "StationName": "MRC35049", + "TxRefAmp": 230.117 +} \ No newline at end of file diff --git a/sub-06/ses-011/anat/sub-06_ses-011_acq-axial_localizer.nii.gz b/sub-06/ses-011/anat/sub-06_ses-011_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..c4cba6d3b --- /dev/null +++ b/sub-06/ses-011/anat/sub-06_ses-011_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Q9/0k/MD5E-s167747--8270078c9496d4f10428ba9415315be9.nii.gz/MD5E-s167747--8270078c9496d4f10428ba9415315be9.nii.gz \ No newline at end of file diff --git a/sub-06/ses-011/anat/sub-06_ses-011_acq-coronal_localizer.json b/sub-06/ses-011/anat/sub-06_ses-011_acq-coronal_localizer.json new file mode 100644 index 000000000..d1b38c2f8 --- /dev/null +++ b/sub-06/ses-011/anat/sub-06_ses-011_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "15:44:14.057500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "ROW", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "Interpolation2D": 1, 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4.5075, + 4.605, + 4.7025, + 4.8025, + 4.9, + 4.9975, + 5.095, + 5.1925, + 5.2925, + 5.39, + 5.4875, + 5.585, + 5.6825, + 5.7825 + ], + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 230.117, + "WipMemBlock": "c25d490c-d295-4b34-adce-547c4408ac1b||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_sbref__part-phase_dup-01.nii.gz b/sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_sbref__part-phase_dup-01.nii.gz new file mode 120000 index 000000000..8cb6f16aa --- /dev/null +++ b/sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_sbref__part-phase_dup-01.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Xg/6j/MD5E-s1103575--b2bc4adb49409f3a6d002b6913c9323a.nii.gz/MD5E-s1103575--b2bc4adb49409f3a6d002b6913c9323a.nii.gz \ No newline at end of file diff --git a/sub-06/ses-011/sub-06_ses-011_scans.tsv b/sub-06/ses-011/sub-06_ses-011_scans.tsv new file mode 120000 index 000000000..08646c6a4 --- /dev/null +++ b/sub-06/ses-011/sub-06_ses-011_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/Xj/PK/MD5E-s3101--48f36f3be111eb4f983656c46edaa148.tsv/MD5E-s3101--48f36f3be111eb4f983656c46edaa148.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..f9a400fd4 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,75 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999235, -0.0356203, 0.0161209, 0.0390854, 0.920685, -0.388345], + "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "SAR": 0.0403265, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "ShimSetting": [626, -7258, -8822, 528, 9, -209, -89, 0], + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 230.117, + "dcmmeta_affine": [ + [-1.9984707832336426, 0.07817082852125168, 0.002018504776060581, 102.85575103759766], + [0.07124060392379761, 1.841369390487671, -0.7773569226264954, -65.21741485595703], + [0.03224172070622444, 0.7766906023025513, 1.8427459001541138, -70.47220611572266], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From c9223750a3bc20509ae5196fd6e0b662bba25383 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:19:25 -0400 Subject: [PATCH 420/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..edfd22671 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = e8fc6dca-d6c9-4200-a536-64fac8a42def diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..d109786e8 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit d109786e8d72aaddce7f0e1d53bcf26388f755dd From bfea956b32001a94557b75488bb4893b2f05e518 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:19:36 -0400 Subject: [PATCH 421/463] fix fmap phase --- ...3_ses-006_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-006_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-006_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-006_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-006_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-03/ses-006/sub-03_ses-006_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-03/ses-006/fmap/{sub-03_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-006_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-006/fmap/{sub-03_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-006_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-006/fmap/sub-03_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-006/fmap/sub-03_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-006/fmap/{sub-03_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-006_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-006/fmap/{sub-03_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-006_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-006/fmap/{sub-03_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-006_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-006/fmap/{sub-03_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-006_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-006/fmap/{sub-03_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-006_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-006/fmap/{sub-03_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-006_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-03/ses-006/fmap/{sub-03_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-03_ses-006_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-03/ses-006/fmap/{sub-03_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-03_ses-006_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-03/ses-006/fmap/{sub-03_ses-006_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-03_ses-006_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-03/ses-006/fmap/{sub-03_ses-006_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-03_ses-006_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-006/fmap/sub-03_ses-006_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-006/fmap/sub-03_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-006/fmap/sub-03_ses-006_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-006/fmap/sub-03_ses-006_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-006/fmap/sub-03_ses-006_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-006/fmap/sub-03_ses-006_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-006/fmap/sub-03_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index a6ab67676..000000000 --- a/sub-03/ses-006/fmap/sub-03_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:54:47.502500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999869, 0.00314417, 0.0158808, 0.00157059, 0.957492, -0.288455], - "ImageOrientationText": "Tra>Cor(-16.8)>Sag(0.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0632482, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [619, -7216, -8762, 695, 68, 0, 8, -6], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.0975, 0.8825, 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a/sub-03/ses-006/fmap/sub-03_ses-006_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Pp/Vz/MD5E-s3334477--fc1be8066aac9f65d5c5959bd10f1cb8.nii.gz/MD5E-s3334477--fc1be8066aac9f65d5c5959bd10f1cb8.nii.gz \ No newline at end of file diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index fa3721a59..000000000 --- a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:54:37.072500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": 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- "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0632482, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 619, - -7216, - -8762, - 695, - 68, - 0, - 8, - -6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 255.562, - "WipMemBlock": "bc4afc8d-c25b-4a24-b1da-99ed44c2425b||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 2ee0512ec..000000000 --- a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/k2/05/MD5E-s1112382--3b5180593b217733196850cff61ffc57.nii.gz/MD5E-s1112382--3b5180593b217733196850cff61ffc57.nii.gz \ No newline at end of file diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 1fc129396..000000000 --- a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:55:43.465000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999869, - 0.00314417, - 0.0158808, - 0.00157059, - 0.957492, - -0.288455 - ], - "ImageOrientationText": 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"RepetitionTime": 1.49, - "SAR": 0.0793077, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 619, - -7216, - -8762, - 695, - 68, - 0, - 8, - -6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 255.562, - "WipMemBlock": "37d1d900-17ee-496c-b1b9-d5e4511c68eb||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 97742c88f..000000000 --- a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/k1/4G/MD5E-s1103751--7dc74781b835e7a21a399e6d899e03b7.nii.gz/MD5E-s1103751--7dc74781b835e7a21a399e6d899e03b7.nii.gz \ No newline at end of file diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 56888beea..000000000 --- a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:08:40.892500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": 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"MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0793077, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 619, - -7216, - -8762, - 695, - 68, - 0, - 8, - -6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 255.562, - "WipMemBlock": "49ca2dfa-5e79-4b8c-86c0-09e5abf0ce17||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index 685f4f659..000000000 --- a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/9z/6q/MD5E-s1103736--3cf5a9c049d5d0c7bc59758b075813ce.nii.gz/MD5E-s1103736--3cf5a9c049d5d0c7bc59758b075813ce.nii.gz \ No newline at end of file diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 2785e96c4..000000000 --- a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:18:12.375000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999869, - 0.00314417, - 0.0158808, - 0.00157059, - 0.957492, - -0.288455 - ], - "ImageOrientationText": "Tra>Cor(-16.8)>Sag(0.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0793077, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 619, - -7216, - -8762, - 695, - 68, - 0, - 8, - -6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 255.562, - "WipMemBlock": "4fa24ce1-bc41-4fac-a927-9a11d2cb2832||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 18f6a18eb..000000000 --- a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/VF/f2/MD5E-s1103762--9f14da3641d803599a825313649db710.nii.gz/MD5E-s1103762--9f14da3641d803599a825313649db710.nii.gz \ No newline at end of file diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 3d20dc831..000000000 --- a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:25:1.157500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999869, - 0.00314417, - 0.0158808, - 0.00157059, - 0.957492, - -0.288455 - ], - "ImageOrientationText": "Tra>Cor(-16.8)>Sag(0.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0793077, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 619, - -7216, - -8762, - 695, - 68, - 0, - 8, - -6 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 255.562, - "WipMemBlock": "d6711c94-9678-4bb4-b448-02c9ae14acad||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index e62a3ae19..000000000 --- a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/75/9W/MD5E-s1103579--ec8e84728cf8014633e54c6a6c01f033.nii.gz/MD5E-s1103579--ec8e84728cf8014633e54c6a6c01f033.nii.gz \ No newline at end of file diff --git a/sub-03/ses-006/sub-03_ses-006_scans.tsv b/sub-03/ses-006/sub-03_ses-006_scans.tsv index 008802c61..2d70866b9 120000 --- a/sub-03/ses-006/sub-03_ses-006_scans.tsv +++ b/sub-03/ses-006/sub-03_ses-006_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/Mw/w9/MD5E-s3321--8e0f979be0b960dfc5c14366b7df3922.tsv/MD5E-s3321--8e0f979be0b960dfc5c14366b7df3922.tsv \ No newline at end of file +../../.git/annex/objects/g2/KX/MD5E-s2599--9a04ece5ab63bb40279b2767bb2d552c.tsv/MD5E-s2599--9a04ece5ab63bb40279b2767bb2d552c.tsv \ No newline at end of file From ab7343dd407898f625add1fb4a4fb863a25dfb8a Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:19:48 -0400 Subject: [PATCH 422/463] fix complex event files --- ...g_events.tsv => sub-03_ses-006_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-03_ses-006_task-mario3_run-02_events.tsv} | 0 .../func/sub-03_ses-006_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-03_ses-006_task-mario3_run-03_events.tsv} | 0 .../func/sub-03_ses-006_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-03_ses-006_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-03/ses-006/func/{sub-03_ses-006_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-006_task-mario3_run-01_events.tsv} (100%) rename sub-03/ses-006/func/{sub-03_ses-006_task-mario3_run-01_part-phase_events.tsv => sub-03_ses-006_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-02_part-phase_events.tsv rename sub-03/ses-006/func/{sub-03_ses-006_task-mario3_run-02_part-mag_events.tsv => sub-03_ses-006_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-02_events.tsv similarity index 100% rename from sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-01_part-phase_events.tsv rename to sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-02_events.tsv diff --git a/sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-02_part-phase_events.tsv b/sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-02_part-mag_events.tsv b/sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-03_events.tsv similarity index 100% rename from sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-02_part-mag_events.tsv rename to sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-03_events.tsv diff --git a/sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-03_part-mag_events.tsv b/sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-03_part-phase_events.tsv b/sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-006/func/sub-03_ses-006_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 04c854d40f9c06d79418ca7cf07c58d7e2ba8129 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:19:49 -0400 Subject: [PATCH 423/463] fix fmap phase --- ...6_ses-011_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-011_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-011_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-011_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-011_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-011_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-011_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-011_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-06/ses-011/sub-06_ses-011_scans.tsv | 2 +- 25 files changed, 1 insertion(+), 944 deletions(-) rename sub-06/ses-011/fmap/{sub-06_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-06_ses-011_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-011/fmap/{sub-06_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-011_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-011/fmap/{sub-06_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-06_ses-011_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-011/fmap/{sub-06_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-011_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-011/fmap/{sub-06_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-06_ses-011_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-06/ses-011/fmap/{sub-06_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-06_ses-011_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-06/ses-011/fmap/{sub-06_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-06_ses-011_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-06/ses-011/fmap/{sub-06_ses-011_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-06_ses-011_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-06/ses-011/fmap/{sub-06_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-06_ses-011_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-06/ses-011/fmap/{sub-06_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-06_ses-011_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-06/ses-011/fmap/{sub-06_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-06_ses-011_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-06/ses-011/fmap/{sub-06_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-06_ses-011_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index ca895bd62..000000000 --- a/sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:45:24.997500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999235, -0.0356203, 0.0161209, 0.0390854, 0.920685, -0.388345], - "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0321606, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": 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0.002018504776060581, 102.85575103759766], - [0.07124060392379761, 1.841369390487671, -0.7773569226264954, -65.21741485595703], - [0.03224172070622444, 0.7766906023025513, 1.8427459001541138, -70.47220611572266], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99923536363111, -0.0356203019993, 0.01612086084824, 0.0390854126061, 0.9206846668406, -0.38834530352], - "ImagePositionPatient": [-866.80487193241, -768.77048605721, 280.50632048563], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.258812, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "154315.971000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.03216055701328, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "154611.667000", - "SliceLocation": -39.478771491479, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000241781, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "154315.897000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["154524.997500", "154526.487500", "154527.977500"], - "ContentTime": ["154611.669000", "154611.672000", "154611.674000"], - "InstanceCreationTime": ["154611.669000", "154611.672000", "154611.674000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4710.0, 4704.0, 4708.0], - "WindowWidth": [18508.0, 18510.0, 18512.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 900e0f998..000000000 --- a/sub-06/ses-011/fmap/sub-06_ses-011_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/zg/QP/MD5E-s3334207--e868d0cc95de4b6173183994df9acf39.nii.gz/MD5E-s3334207--e868d0cc95de4b6173183994df9acf39.nii.gz \ No newline at end of file diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 5c5e74e1c..000000000 --- a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:45:14.567500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999235, - -0.0356203, - 0.0161209, - 0.0390854, - 0.920685, - -0.388345 - ], - "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0321606, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 626, - -7258, - -8822, - 528, - 9, - -209, - -89, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 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a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/XZ/1X/MD5E-s1112266--1fa6b013c3d7cc313e5d3e5492eadd21.nii.gz/MD5E-s1112266--1fa6b013c3d7cc313e5d3e5492eadd21.nii.gz \ No newline at end of file diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index dd6b22976..000000000 --- a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:46:37.390000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": 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a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "15:54:55.845000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999235, - -0.0356203, - 0.0161209, - 0.0390854, - 0.920685, - -0.388345 - ], - "ImageOrientationText": 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sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 1057e0325..000000000 --- a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:05:10.995000", - "BandwidthPerPixelPhaseEncode": 17.17, - 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a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 8cb6f16aa..000000000 --- a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Xg/6j/MD5E-s1103575--b2bc4adb49409f3a6d002b6913c9323a.nii.gz/MD5E-s1103575--b2bc4adb49409f3a6d002b6913c9323a.nii.gz \ No newline at end of file diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 620643301..000000000 --- a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:07:37.420000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999235, - -0.0356203, - 0.0161209, - 0.0390854, - 0.920685, - -0.388345 - ], - "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0403265, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 16, - "ShimSetting": [ - 626, - -7258, - -8822, - 528, - 9, - -209, - -89, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 230.117, - "WipMemBlock": "bd073f7e-e88f-44fc-aed2-8de6dfa5b973||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 6875fcaf6..000000000 --- a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Q4/X6/MD5E-s1103688--b91ba5457477461fd7caedcfafcb8708.nii.gz/MD5E-s1103688--b91ba5457477461fd7caedcfafcb8708.nii.gz \ No newline at end of file diff --git a/sub-06/ses-011/sub-06_ses-011_scans.tsv b/sub-06/ses-011/sub-06_ses-011_scans.tsv index 08646c6a4..3ba6fa299 120000 --- a/sub-06/ses-011/sub-06_ses-011_scans.tsv +++ b/sub-06/ses-011/sub-06_ses-011_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/Xj/PK/MD5E-s3101--48f36f3be111eb4f983656c46edaa148.tsv/MD5E-s3101--48f36f3be111eb4f983656c46edaa148.tsv \ No newline at end of file +../../.git/annex/objects/fk/F8/MD5E-s2381--fe66c1f112e493e1c61b2ac731b6cb58.tsv/MD5E-s2381--fe66c1f112e493e1c61b2ac731b6cb58.tsv \ No newline at end of file From b305f285399a7a54f0e9c382d26d724351427ea8 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:20:00 -0400 Subject: [PATCH 424/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-03_ses-002_acq-axial_localizer.json | 81 +++ .../sub-03_ses-002_acq-axial_localizer.nii.gz | 1 + ...3_ses-002_acq-axial_localizer__dup-01.json | 81 +++ ...ses-002_acq-axial_localizer__dup-01.nii.gz | 1 + .../sub-03_ses-002_acq-coronal_localizer.json | 81 +++ ...ub-03_ses-002_acq-coronal_localizer.nii.gz | 1 + ...ses-002_acq-coronal_localizer__dup-01.json | 81 +++ ...s-002_acq-coronal_localizer__dup-01.nii.gz | 1 + ...sub-03_ses-002_acq-sagittal_localizer.json | 86 +++ ...b-03_ses-002_acq-sagittal_localizer.nii.gz | 1 + ...es-002_acq-sagittal_localizer__dup-01.json | 86 +++ ...-002_acq-sagittal_localizer__dup-01.nii.gz | 1 + sub-03/ses-002/anat/sub-03_ses-002_scout.json | 542 ++++++++++++++++++ .../ses-002/anat/sub-03_ses-002_scout.nii.gz | 1 + .../anat/sub-03_ses-002_scout__dup-01.json | 542 ++++++++++++++++++ .../anat/sub-03_ses-002_scout__dup-01.nii.gz | 1 + ...2_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...ld_dir-AP_run-01_part-mag_epi__dup-01.json | 171 ++++++ ..._dir-AP_run-01_part-mag_epi__dup-01.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._dir-AP_run-01_part-phase_epi__dup-01.json | 177 ++++++ ...ir-AP_run-01_part-phase_epi__dup-01.nii.gz | 1 + ...ef_dir-AP_run-01_epi__part-mag_dup-01.json | 149 +++++ ..._dir-AP_run-01_epi__part-mag_dup-01.nii.gz | 1 + ..._dir-AP_run-01_epi__part-phase_dup-01.json | 152 +++++ ...ir-AP_run-01_epi__part-phase_dup-01.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ...-002_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-01_part-mag_events.tsv | 1 + ...002_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-01_part-phase_events.tsv | 1 + ...2_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-002_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...002_task-mario3_run-02_part-mag_events.tsv | 1 + ...002_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...2_task-mario3_run-02_part-phase_events.tsv | 1 + ...2_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-002_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...02_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...k-mario3_run-03_part-mag_bold__dup-01.json | 172 ++++++ ...mario3_run-03_part-mag_bold__dup-01.nii.gz | 1 + ...002_task-mario3_run-03_part-mag_events.tsv | 1 + ...002_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...2_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...02_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...mario3_run-03_part-phase_bold__dup-01.json | 178 ++++++ ...rio3_run-03_part-phase_bold__dup-01.nii.gz | 1 + ...2_task-mario3_run-03_part-phase_events.tsv | 1 + ...2_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-mario3_run-03_sbref__part-mag_dup-01.json | 150 +++++ ...ario3_run-03_sbref__part-mag_dup-01.nii.gz | 1 + ...ario3_run-03_sbref__part-phase_dup-01.json | 153 +++++ ...io3_run-03_sbref__part-phase_dup-01.nii.gz | 1 + sub-03/ses-002/sub-03_ses-002_scans.tsv | 1 + task-mario3_bold.json | 64 +++ 93 files changed, 6843 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-03/ses-002/anat/sub-03_ses-002_acq-axial_localizer.json create mode 120000 sub-03/ses-002/anat/sub-03_ses-002_acq-axial_localizer.nii.gz create mode 100644 sub-03/ses-002/anat/sub-03_ses-002_acq-axial_localizer__dup-01.json create mode 120000 sub-03/ses-002/anat/sub-03_ses-002_acq-axial_localizer__dup-01.nii.gz create mode 100644 sub-03/ses-002/anat/sub-03_ses-002_acq-coronal_localizer.json create mode 120000 sub-03/ses-002/anat/sub-03_ses-002_acq-coronal_localizer.nii.gz create mode 100644 sub-03/ses-002/anat/sub-03_ses-002_acq-coronal_localizer__dup-01.json create mode 120000 sub-03/ses-002/anat/sub-03_ses-002_acq-coronal_localizer__dup-01.nii.gz create mode 100644 sub-03/ses-002/anat/sub-03_ses-002_acq-sagittal_localizer.json create mode 120000 sub-03/ses-002/anat/sub-03_ses-002_acq-sagittal_localizer.nii.gz create mode 100644 sub-03/ses-002/anat/sub-03_ses-002_acq-sagittal_localizer__dup-01.json create mode 120000 sub-03/ses-002/anat/sub-03_ses-002_acq-sagittal_localizer__dup-01.nii.gz create mode 100644 sub-03/ses-002/anat/sub-03_ses-002_scout.json create mode 120000 sub-03/ses-002/anat/sub-03_ses-002_scout.nii.gz create mode 100644 sub-03/ses-002/anat/sub-03_ses-002_scout__dup-01.json create mode 120000 sub-03/ses-002/anat/sub-03_ses-002_scout__dup-01.nii.gz create mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-mag_epi__dup-01.json create mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-mag_epi__dup-01.nii.gz create mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-phase_epi__dup-01.json create mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-phase_epi__dup-01.nii.gz create mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__part-mag_dup-01.json create mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__part-mag_dup-01.nii.gz create mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__part-phase_dup-01.json create mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__part-phase_dup-01.nii.gz create mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-01_part-mag_bold.nii.gz create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-01_part-phase_bold.nii.gz create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_part-mag_events.tsv create mode 100644 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_part-mag_sbref.json create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_part-phase_bold.json create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_part-phase_bold.nii.gz create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_part-phase_events.tsv create mode 100644 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_part-phase_sbref.json create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_part-phase_sbref.nii.gz create mode 100644 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-mag_bold.json create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-mag_bold.nii.gz create mode 100644 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-mag_bold__dup-01.json create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-mag_bold__dup-01.nii.gz create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-mag_events.tsv create mode 100644 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-mag_sbref.json create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-mag_sbref.nii.gz create mode 100644 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-phase_bold.json create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-phase_bold.nii.gz create mode 100644 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-phase_bold__dup-01.json create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-phase_bold__dup-01.nii.gz create mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-phase_events.tsv create mode 100644 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--- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..18a159816 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-03 43 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-03/ses-002/anat/sub-03_ses-002_acq-axial_localizer.json b/sub-03/ses-002/anat/sub-03_ses-002_acq-axial_localizer.json new file mode 100644 index 000000000..0fc35eb88 --- /dev/null +++ b/sub-03/ses-002/anat/sub-03_ses-002_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + 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newline at end of file diff --git a/sub-03/ses-002/anat/sub-03_ses-002_acq-axial_localizer.nii.gz b/sub-03/ses-002/anat/sub-03_ses-002_acq-axial_localizer.nii.gz new file mode 120000 index 000000000..370ee4f14 --- /dev/null +++ b/sub-03/ses-002/anat/sub-03_ses-002_acq-axial_localizer.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/FZ/Qp/MD5E-s164958--a2c48220e29e1110b44e49217af3d02c.nii.gz/MD5E-s164958--a2c48220e29e1110b44e49217af3d02c.nii.gz \ No newline at end of file diff --git a/sub-03/ses-002/anat/sub-03_ses-002_acq-axial_localizer__dup-01.json b/sub-03/ses-002/anat/sub-03_ses-002_acq-axial_localizer__dup-01.json new file mode 100644 index 000000000..8898a69a8 --- /dev/null +++ b/sub-03/ses-002/anat/sub-03_ses-002_acq-axial_localizer__dup-01.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "13:47:15.077500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + 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000000000..6f0f857a3 --- /dev/null +++ b/sub-03/ses-002/anat/sub-03_ses-002_acq-axial_localizer__dup-01.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Jj/1p/MD5E-s166464--1cb9df005212e96dfe2afce23e0aa0c9.nii.gz/MD5E-s166464--1cb9df005212e96dfe2afce23e0aa0c9.nii.gz \ No newline at end of file diff --git a/sub-03/ses-002/anat/sub-03_ses-002_acq-coronal_localizer.json b/sub-03/ses-002/anat/sub-03_ses-002_acq-coronal_localizer.json new file mode 100644 index 000000000..21a64a7bf --- /dev/null +++ b/sub-03/ses-002/anat/sub-03_ses-002_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "14:16:30.982500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + 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b/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_sbref__part-phase_dup-01.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "14:18:24.307500", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTime1": 0.037, + "EchoTime2": 0.001, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Single-band reference", + "ImageOrientationPatientDICOM": [ + 0.999763, + 0.0153954, + 0.0154198, + -0.010819, + 0.965003, + -0.262017 + ], + "ImageOrientationText": "Tra>Cor(-15.2)>Sag(1.1)", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "P", + "ND", + "MOSAIC", + "PHASE" + ], + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "ProtocolName": "func_task-mario3_run-03", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + 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"mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 210.273, + "WipMemBlock": "b50a4c5c-798e-4658-b091-b24b5228d6d9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" +} \ No newline at end of file diff --git a/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_sbref__part-phase_dup-01.nii.gz b/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_sbref__part-phase_dup-01.nii.gz new file mode 120000 index 000000000..4accc921c --- /dev/null +++ b/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_sbref__part-phase_dup-01.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/Kk/qV/MD5E-s1103666--b9c4c24a56166848fd8ff76eda6114f9.nii.gz/MD5E-s1103666--b9c4c24a56166848fd8ff76eda6114f9.nii.gz \ No newline at end of file diff --git a/sub-03/ses-002/sub-03_ses-002_scans.tsv b/sub-03/ses-002/sub-03_ses-002_scans.tsv new file mode 120000 index 000000000..d87f0f67c --- /dev/null +++ b/sub-03/ses-002/sub-03_ses-002_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/mK/Mg/MD5E-s4150--91901794bf9b5b0c0166c0341c9df4d6.tsv/MD5E-s4150--91901794bf9b5b0c0166c0341c9df4d6.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..c2df6e4b1 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,64 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From a332effe7b7f09aaa9bd3db8b5a4d38415f97f99 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:20:01 -0400 Subject: [PATCH 425/463] fill IntendedFor --- ...3_ses-006_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...3_ses-006_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...3_ses-006_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...3_ses-006_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_epi.json index a40b16d8e..a516424ad 100644 --- a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999869, - 0.00314417, - 0.0158808, - 0.00157059, - 0.957492, - -0.288455 - ], + "ImageOrientationPatientDICOM": [0.999869, 0.00314417, 0.0158808, 0.00157059, 0.957492, -0.288455], "ImageOrientationText": "Tra>Cor(-16.8)>Sag(0.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-03_ses-006_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-006/func/sub-03_ses-006_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-006/func/sub-03_ses-006_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 619, - -7216, - -8762, - 695, - 68, - 0, - 8, - -6 - ], + "ShimSetting": [619, -7216, -8762, 695, 68, 0, 8, -6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_epi.json b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_epi.json index a7007f41b..253e8e458 100644 --- a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999869, - 0.00314417, - 0.0158808, - 0.00157059, - 0.957492, - -0.288455 - ], + "ImageOrientationPatientDICOM": [0.999869, 0.00314417, 0.0158808, 0.00157059, 0.957492, -0.288455], "ImageOrientationText": "Tra>Cor(-16.8)>Sag(0.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-03_ses-006_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 619, - -7216, - -8762, - 695, - 68, - 0, - 8, - -6 - ], + "ShimSetting": [619, -7216, -8762, 695, 68, 0, 8, -6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_epi.json b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_epi.json index 51ded5ca4..1f92176a4 100644 --- a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999869, - 0.00314417, - 0.0158808, - 0.00157059, - 0.957492, - -0.288455 - ], + "ImageOrientationPatientDICOM": [0.999869, 0.00314417, 0.0158808, 0.00157059, 0.957492, -0.288455], "ImageOrientationText": "Tra>Cor(-16.8)>Sag(0.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-03_ses-006_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 619, - -7216, - -8762, - 695, - 68, - 0, - 8, - -6 - ], + "ShimSetting": [619, -7216, -8762, 695, 68, 0, 8, -6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_epi.json b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_epi.json index cd6c2a6a5..d5671c7e2 100644 --- a/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-03/ses-006/fmap/sub-03_ses-006_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999869, - 0.00314417, - 0.0158808, - 0.00157059, - 0.957492, - -0.288455 - ], + "ImageOrientationPatientDICOM": [0.999869, 0.00314417, 0.0158808, 0.00157059, 0.957492, -0.288455], "ImageOrientationText": "Tra>Cor(-16.8)>Sag(0.9)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-006/func/sub-03_ses-006_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 619, - -7216, - -8762, - 695, - 68, - 0, - 8, - -6 - ], + "ShimSetting": [619, -7216, -8762, 695, 68, 0, 8, -6], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From e2bc70dad39c4b1870dae9748815231ee1e4da75 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:20:02 -0400 Subject: [PATCH 426/463] fix complex event files --- ...g_events.tsv => sub-06_ses-011_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-06_ses-011_task-mario3_run-02_events.tsv} | 0 .../func/sub-06_ses-011_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-06_ses-011_task-mario3_run-03_events.tsv} | 0 .../func/sub-06_ses-011_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-06_ses-011_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-06/ses-011/func/{sub-06_ses-011_task-mario3_run-01_part-mag_events.tsv => sub-06_ses-011_task-mario3_run-01_events.tsv} (100%) rename sub-06/ses-011/func/{sub-06_ses-011_task-mario3_run-01_part-phase_events.tsv => sub-06_ses-011_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-02_part-phase_events.tsv rename sub-06/ses-011/func/{sub-06_ses-011_task-mario3_run-02_part-mag_events.tsv => sub-06_ses-011_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-01_part-mag_events.tsv b/sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-01_events.tsv similarity index 100% rename from sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-01_part-mag_events.tsv rename to sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-01_events.tsv diff --git a/sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-01_part-phase_events.tsv b/sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-02_events.tsv similarity index 100% rename from sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-01_part-phase_events.tsv rename to sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-02_events.tsv diff --git a/sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-02_part-phase_events.tsv b/sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-02_part-mag_events.tsv b/sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_events.tsv similarity index 100% rename from sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-02_part-mag_events.tsv rename to sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_events.tsv diff --git a/sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_part-mag_events.tsv b/sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_part-phase_events.tsv b/sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-011/func/sub-06_ses-011_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 4a708c5842d581b0782e7ac5a40e50c25557bbc5 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:20:23 -0400 Subject: [PATCH 427/463] fill IntendedFor --- ...6_ses-011_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...6_ses-011_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...6_ses-011_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...6_ses-011_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_epi.json b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_epi.json index eaf4b75de..552df3649 100644 --- a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999235, - -0.0356203, - 0.0161209, - 0.0390854, - 0.920685, - -0.388345 - ], + "ImageOrientationPatientDICOM": [0.999235, -0.0356203, 0.0161209, 0.0390854, 0.920685, -0.388345], "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-06_ses-011_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-011/func/sub-06_ses-011_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-011/func/sub-06_ses-011_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 626, - -7258, - -8822, - 528, - 9, - -209, - -89, - 0 - ], + "ShimSetting": [626, -7258, -8822, 528, 9, -209, -89, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_epi.json b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_epi.json index d4a3198e6..05f1268bf 100644 --- a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999235, - -0.0356203, - 0.0161209, - 0.0390854, - 0.920685, - -0.388345 - ], + "ImageOrientationPatientDICOM": [0.999235, -0.0356203, 0.0161209, 0.0390854, 0.920685, -0.388345], "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-06_ses-011_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 626, - -7258, - -8822, - 528, - 9, - -209, - -89, - 0 - ], + "ShimSetting": [626, -7258, -8822, 528, 9, -209, -89, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-02_epi.json b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-02_epi.json index 8232626b7..be79cec47 100644 --- a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999235, - -0.0356203, - 0.0161209, - 0.0390854, - 0.920685, - -0.388345 - ], + "ImageOrientationPatientDICOM": [0.999235, -0.0356203, 0.0161209, 0.0390854, 0.920685, -0.388345], "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-06_ses-011_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 626, - -7258, - -8822, - 528, - 9, - -209, - -89, - 0 - ], + "ShimSetting": [626, -7258, -8822, 528, 9, -209, -89, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_epi.json b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_epi.json index b253c85a4..d7c8499df 100644 --- a/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-06/ses-011/fmap/sub-06_ses-011_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999235, - -0.0356203, - 0.0161209, - 0.0390854, - 0.920685, - -0.388345 - ], + "ImageOrientationPatientDICOM": [0.999235, -0.0356203, 0.0161209, 0.0390854, 0.920685, -0.388345], "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-011/func/sub-06_ses-011_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 16, - "ShimSetting": [ - 626, - -7258, - -8822, - 528, - 9, - -209, - -89, - 0 - ], + "ShimSetting": [626, -7258, -8822, 528, 9, -209, -89, 0], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 141d99694847ba61088264973eb47b5adb5f5606 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:21:31 -0400 Subject: [PATCH 428/463] fix fmap phase --- ...3_ses-002_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-002_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...2_acq-bold_dir-AP_run-01_epi__dup-01.json} | 0 ...acq-bold_dir-AP_run-01_epi__dup-01.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._dir-AP_run-01_part-phase_epi__dup-01.json | 177 ------------------ ...ir-AP_run-01_part-phase_epi__dup-01.nii.gz | 1 - ..._ses-002_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-002_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ..._acq-sbref_dir-AP_run-01_epi__dup-01.json} | 0 ...cq-sbref_dir-AP_run-01_epi__dup-01.nii.gz} | 0 ..._dir-AP_run-01_epi__part-phase_dup-01.json | 152 --------------- ...ir-AP_run-01_epi__part-phase_dup-01.nii.gz | 1 - ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-002_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-002_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - sub-03/ses-002/sub-03_ses-002_scans.tsv | 2 +- 33 files changed, 1 insertion(+), 1275 deletions(-) rename sub-03/ses-002/fmap/{sub-03_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-03_ses-002_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-002/fmap/{sub-03_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-002_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) rename sub-03/ses-002/fmap/{sub-03_ses-002_acq-bold_dir-AP_run-01_part-mag_epi__dup-01.json => sub-03_ses-002_acq-bold_dir-AP_run-01_epi__dup-01.json} (100%) rename sub-03/ses-002/fmap/{sub-03_ses-002_acq-bold_dir-AP_run-01_part-mag_epi__dup-01.nii.gz => sub-03_ses-002_acq-bold_dir-AP_run-01_epi__dup-01.nii.gz} (100%) delete mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz delete mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-phase_epi__dup-01.json delete mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-phase_epi__dup-01.nii.gz rename sub-03/ses-002/fmap/{sub-03_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-03_ses-002_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-03/ses-002/fmap/{sub-03_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-03_ses-002_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) rename sub-03/ses-002/fmap/{sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__part-mag_dup-01.json => sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__dup-01.json} (100%) rename sub-03/ses-002/fmap/{sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__part-mag_dup-01.nii.gz => sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__dup-01.nii.gz} (100%) delete mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__part-phase_dup-01.json delete mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__part-phase_dup-01.nii.gz delete mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-03/ses-002/fmap/{sub-03_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-03_ses-002_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-03/ses-002/fmap/{sub-03_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-03_ses-002_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-03/ses-002/fmap/{sub-03_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-03_ses-002_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-03/ses-002/fmap/{sub-03_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-03_ses-002_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-03/ses-002/fmap/{sub-03_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-03_ses-002_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-03/ses-002/fmap/{sub-03_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-03_ses-002_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-03/ses-002/fmap/{sub-03_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-03_ses-002_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-03/ses-002/fmap/{sub-03_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-03_ses-002_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-mag_epi__dup-01.json b/sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_epi__dup-01.json similarity index 100% rename from sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-mag_epi__dup-01.json rename to sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_epi__dup-01.json diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-mag_epi__dup-01.nii.gz b/sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_epi__dup-01.nii.gz similarity index 100% rename from sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-mag_epi__dup-01.nii.gz rename to sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_epi__dup-01.nii.gz diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 0068a81ff..000000000 --- a/sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:17:22.785000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": 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+++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/1x/0M/MD5E-s3334911--6d3752f740a58c528d8f32b5a9fc1b66.nii.gz/MD5E-s3334911--6d3752f740a58c528d8f32b5a9fc1b66.nii.gz \ No newline at end of file diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-phase_epi__dup-01.json b/sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-phase_epi__dup-01.json deleted file mode 100644 index 2fceab3f3..000000000 --- a/sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-phase_epi__dup-01.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:48:14.997500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - 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"Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["134814.997500", "134816.487500", "134817.977500"], - "ContentTime": ["134901.610000", "134901.613000", "134901.615000"], - "InstanceCreationTime": ["134901.610000", "134901.613000", "134901.615000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4854.0, 4860.0, 4854.0], - "WindowWidth": [18610.0, 18616.0, 18612.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-phase_epi__dup-01.nii.gz b/sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-phase_epi__dup-01.nii.gz deleted file mode 120000 index 87eac0125..000000000 --- a/sub-03/ses-002/fmap/sub-03_ses-002_acq-bold_dir-AP_run-01_part-phase_epi__dup-01.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/m9/mm/MD5E-s3334866--ee6ed2ae9b8389e3d5268d94b06662d3.nii.gz/MD5E-s3334866--ee6ed2ae9b8389e3d5268d94b06662d3.nii.gz \ No newline at end of file diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__part-mag_dup-01.json b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__dup-01.json similarity index 100% rename from sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__part-mag_dup-01.json rename to sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__dup-01.json diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__part-mag_dup-01.nii.gz b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__dup-01.nii.gz similarity index 100% rename from sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__part-mag_dup-01.nii.gz rename to sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__dup-01.nii.gz diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__part-phase_dup-01.json b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__part-phase_dup-01.json deleted file mode 100644 index b9c18e401..000000000 --- a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__part-phase_dup-01.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:48:4.567500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999724, - 0.0205693, - 0.0113346, - -0.0167522, - 0.962805, - -0.269678 - ], - "ImageOrientationText": 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"RepetitionTime": 1.49, - "SAR": 0.0428189, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 638, - -7205, - -8736, - 692, - 70, - 38, - -12, - -14 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 226.876, - "WipMemBlock": "90f6da48-34a1-4937-972a-2216f80c8dde||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__part-phase_dup-01.nii.gz b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__part-phase_dup-01.nii.gz deleted file mode 120000 index cd989e650..000000000 --- a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi__part-phase_dup-01.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/jJ/3k/MD5E-s1112457--867a03d6fa7c686bad6b337ec5dfc422.nii.gz/MD5E-s1112457--867a03d6fa7c686bad6b337ec5dfc422.nii.gz \ No newline at end of file diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 62284fab4..000000000 --- a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:17:12.355000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999763, - 0.0153954, - 0.0154198, - -0.010819, - 0.965003, - -0.262017 - ], - "ImageOrientationText": "Tra>Cor(-15.2)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0315893, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 20, - "ShimSetting": [ - 641, - -7223, - -8735, - 708, - 70, - -18, - 50, - -13 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 210.273, - "WipMemBlock": "d2ad8cba-9d84-4af8-9e96-e67edee47783||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 6b725e13a..000000000 --- a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/kJ/28/MD5E-s1112227--c4f03b8fae5648e297be5dd3c633f8f7.nii.gz/MD5E-s1112227--c4f03b8fae5648e297be5dd3c633f8f7.nii.gz \ No newline at end of file diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index ee69fee25..000000000 --- a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:49:27.492500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999724, - 0.0205693, - 0.0113346, - -0.0167522, - 0.962805, - -0.269678 - ], - "ImageOrientationText": "Tra>Cor(-15.6)>Sag(0.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0536912, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 638, - -7205, - -8736, - 692, - 70, - 38, - -12, - -14 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 226.876, - "WipMemBlock": "bd20858d-3872-48e0-968b-06f2c83eb300||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index af61f1606..000000000 --- a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/v2/26/MD5E-s1103812--b82cb51eb8af34172eed576519aed939.nii.gz/MD5E-s1103812--b82cb51eb8af34172eed576519aed939.nii.gz \ No newline at end of file diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index e468e4507..000000000 --- a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "13:59:16.957500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999724, - 0.0205693, - 0.0113346, - -0.0167522, - 0.962805, - -0.269678 - ], - "ImageOrientationText": "Tra>Cor(-15.6)>Sag(0.9)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0536912, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 638, - -7205, - -8736, - 692, - 70, - 38, - -12, - -14 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 226.876, - "WipMemBlock": "63985315-62c6-4cfa-8c87-85a8c28b551d||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index af5640ed2..000000000 --- a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/jK/V0/MD5E-s1103772--00a85ada7ea003d9d74ea730b600870e.nii.gz/MD5E-s1103772--00a85ada7ea003d9d74ea730b600870e.nii.gz \ No newline at end of file diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index acc58c0b4..000000000 --- a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:18:24.307500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999763, - 0.0153954, - 0.0154198, - -0.010819, - 0.965003, - -0.262017 - ], - "ImageOrientationText": "Tra>Cor(-15.2)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0396103, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 23, - "ShimSetting": [ - 641, - -7223, - -8735, - 708, - 70, - -18, - 50, - -13 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 210.273, - "WipMemBlock": "b50a4c5c-798e-4658-b091-b24b5228d6d9||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 4accc921c..000000000 --- a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Kk/qV/MD5E-s1103666--b9c4c24a56166848fd8ff76eda6114f9.nii.gz/MD5E-s1103666--b9c4c24a56166848fd8ff76eda6114f9.nii.gz \ No newline at end of file diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index fd3ec9297..000000000 --- a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "14:25:17.020000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999763, - 0.0153954, - 0.0154198, - -0.010819, - 0.965003, - -0.262017 - ], - "ImageOrientationText": "Tra>Cor(-15.2)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0396103, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 26, - "ShimSetting": [ - 641, - -7223, - -8735, - 708, - 70, - -18, - 50, - -13 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 210.273, - "WipMemBlock": "b5159d50-2533-417b-9371-f31fa3018fc3||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index c358b1918..000000000 --- a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/mz/90/MD5E-s1103729--9ebfd8f0d1a7cd07ab4cdffe1ab1c19a.nii.gz/MD5E-s1103729--9ebfd8f0d1a7cd07ab4cdffe1ab1c19a.nii.gz \ No newline at end of file diff --git a/sub-03/ses-002/sub-03_ses-002_scans.tsv b/sub-03/ses-002/sub-03_ses-002_scans.tsv index d87f0f67c..31441cde1 120000 --- a/sub-03/ses-002/sub-03_ses-002_scans.tsv +++ b/sub-03/ses-002/sub-03_ses-002_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/mK/Mg/MD5E-s4150--91901794bf9b5b0c0166c0341c9df4d6.tsv/MD5E-s4150--91901794bf9b5b0c0166c0341c9df4d6.tsv \ No newline at end of file +../../.git/annex/objects/Gm/1W/MD5E-s3175--c18eac64d5fca602df5276ef96d0bd65.tsv/MD5E-s3175--c18eac64d5fca602df5276ef96d0bd65.tsv \ No newline at end of file From ce5fde22240a4789b7d8601ae366156d93b2e6f6 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:21:44 -0400 Subject: [PATCH 429/463] fix complex event files --- ...g_events.tsv => sub-03_ses-002_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-03_ses-002_task-mario3_run-02_events.tsv} | 0 .../func/sub-03_ses-002_task-mario3_run-02_part-phase_events.tsv | 1 - ...g_events.tsv => sub-03_ses-002_task-mario3_run-03_events.tsv} | 0 .../func/sub-03_ses-002_task-mario3_run-03_part-mag_events.tsv | 1 - .../func/sub-03_ses-002_task-mario3_run-03_part-phase_events.tsv | 1 - 6 files changed, 3 deletions(-) rename sub-03/ses-002/func/{sub-03_ses-002_task-mario3_run-01_part-mag_events.tsv => sub-03_ses-002_task-mario3_run-01_events.tsv} (100%) rename sub-03/ses-002/func/{sub-03_ses-002_task-mario3_run-01_part-phase_events.tsv => sub-03_ses-002_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_part-phase_events.tsv rename sub-03/ses-002/func/{sub-03_ses-002_task-mario3_run-02_part-mag_events.tsv => sub-03_ses-002_task-mario3_run-03_events.tsv} (100%) delete mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-mag_events.tsv delete mode 120000 sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-phase_events.tsv diff --git a/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-01_part-mag_events.tsv b/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-01_events.tsv similarity index 100% rename from sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-01_part-mag_events.tsv rename to sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-01_events.tsv diff --git a/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-01_part-phase_events.tsv b/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_events.tsv similarity index 100% rename from sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-01_part-phase_events.tsv rename to sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_events.tsv diff --git a/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_part-phase_events.tsv b/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_part-mag_events.tsv b/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_events.tsv similarity index 100% rename from sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_part-mag_events.tsv rename to sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_events.tsv diff --git a/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-mag_events.tsv b/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-phase_events.tsv b/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-03_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From dcf1d53431d2b9d86d4b8640b3c30e8073f7eabb Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:21:57 -0400 Subject: [PATCH 430/463] fill IntendedFor --- ...3_ses-002_acq-sbref_dir-AP_run-01_epi.json | 88 ++----------------- ...3_ses-002_acq-sbref_dir-PA_run-04_epi.json | 88 ++----------------- 2 files changed, 14 insertions(+), 162 deletions(-) diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi.json b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi.json index 8e9f8adf6..c0e0589a5 100644 --- a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999763, - 0.0153954, - 0.0154198, - -0.010819, - 0.965003, - -0.262017 - ], + "ImageOrientationPatientDICOM": [0.999763, 0.0153954, 0.0154198, -0.010819, 0.965003, -0.262017], "ImageOrientationText": "Tra>Cor(-15.2)>Sag(1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-03_ses-002_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 20, - "ShimSetting": [ - 641, - -7223, - -8735, - 708, - 70, - -18, - 50, - -13 - ], + "ShimSetting": [641, -7223, -8735, 708, 70, -18, 50, -13], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_epi.json b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_epi.json index 16ccc1300..8db8addf5 100644 --- a/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-03/ses-002/fmap/sub-03_ses-002_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999763, - 0.0153954, - 0.0154198, - -0.010819, - 0.965003, - -0.262017 - ], + "ImageOrientationPatientDICOM": [0.999763, 0.0153954, 0.0154198, -0.010819, 0.965003, -0.262017], "ImageOrientationText": "Tra>Cor(-15.2)>Sag(1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-002/func/sub-03_ses-002_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 26, - "ShimSetting": [ - 641, - -7223, - -8735, - 708, - 70, - -18, - 50, - -13 - ], + "ShimSetting": [641, -7223, -8735, 708, 70, -18, 50, -13], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From bc08313bf7c7e0cb04f97a542dcb300545bba505 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:30:51 -0400 Subject: [PATCH 431/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..7c2549bbc --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = d83cf2b3-1563-45ef-a3d7-e8ff669ea00a diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..51d636b47 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 51d636b47303360376a038871f2ffebde56645e4 From 288aa2215056ae49711227a1c8323598312668dd Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:31:15 -0400 Subject: [PATCH 432/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-06_ses-017_acq-axial_localizer.json | 81 +++ .../sub-06_ses-017_acq-axial_localizer.nii.gz | 1 + .../sub-06_ses-017_acq-coronal_localizer.json | 81 +++ ...ub-06_ses-017_acq-coronal_localizer.nii.gz | 1 + ...sub-06_ses-017_acq-sagittal_localizer.json | 86 +++ ...b-06_ses-017_acq-sagittal_localizer.nii.gz | 1 + sub-06/ses-017/anat/sub-06_ses-017_scout.json | 542 ++++++++++++++++++ .../ses-017/anat/sub-06_ses-017_scout.nii.gz | 1 + ...7_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ...-017_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...k-mario3_run-01_part-mag_bold__dup-01.json | 172 ++++++ ...mario3_run-01_part-mag_bold__dup-01.nii.gz | 1 + ...017_task-mario3_run-01_part-mag_events.tsv | 1 + ...017_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...mario3_run-01_part-phase_bold__dup-01.json | 178 ++++++ ...rio3_run-01_part-phase_bold__dup-01.nii.gz | 1 + ...7_task-mario3_run-01_part-phase_events.tsv | 1 + ...7_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-mario3_run-01_sbref__part-mag_dup-01.json | 150 +++++ ...ario3_run-01_sbref__part-mag_dup-01.nii.gz | 1 + ...ario3_run-01_sbref__part-phase_dup-01.json | 153 +++++ ...io3_run-01_sbref__part-phase_dup-01.nii.gz | 1 + ...-017_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...17_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...017_task-mario3_run-02_part-mag_events.tsv | 1 + ...017_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...7_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...17_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...7_task-mario3_run-02_part-phase_events.tsv | 1 + ...7_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + sub-06/ses-017/sub-06_ses-017_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 63 files changed, 4445 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-06/ses-017/anat/sub-06_ses-017_acq-axial_localizer.json create mode 120000 sub-06/ses-017/anat/sub-06_ses-017_acq-axial_localizer.nii.gz create mode 100644 sub-06/ses-017/anat/sub-06_ses-017_acq-coronal_localizer.json create mode 120000 sub-06/ses-017/anat/sub-06_ses-017_acq-coronal_localizer.nii.gz create mode 100644 sub-06/ses-017/anat/sub-06_ses-017_acq-sagittal_localizer.json create mode 120000 sub-06/ses-017/anat/sub-06_ses-017_acq-sagittal_localizer.nii.gz create mode 100644 sub-06/ses-017/anat/sub-06_ses-017_scout.json create mode 120000 sub-06/ses-017/anat/sub-06_ses-017_scout.nii.gz create mode 100644 sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_part-mag_bold.json create mode 120000 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_part-mag_bold.nii.gz create mode 100644 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_part-mag_bold__dup-01.json create mode 120000 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_part-mag_bold__dup-01.nii.gz create mode 120000 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_part-mag_events.tsv create mode 100644 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_part-mag_sbref.json create mode 120000 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_part-mag_sbref.nii.gz create mode 100644 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_part-phase_bold.json create mode 120000 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_part-phase_bold.nii.gz create mode 100644 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_part-phase_bold__dup-01.json create mode 120000 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_part-phase_bold__dup-01.nii.gz create mode 120000 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_part-phase_events.tsv create mode 100644 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_part-phase_sbref.json create mode 120000 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_part-phase_sbref.nii.gz create mode 100644 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_sbref__part-mag_dup-01.json create mode 120000 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_sbref__part-mag_dup-01.nii.gz create mode 100644 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_sbref__part-phase_dup-01.json create mode 120000 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_sbref__part-phase_dup-01.nii.gz create mode 100644 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-02_part-mag_bold.json create mode 120000 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-02_part-mag_bold.nii.gz create mode 120000 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-02_part-mag_events.tsv create mode 100644 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a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..db37a3f34 --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-06 41 F control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-06/ses-017/anat/sub-06_ses-017_acq-axial_localizer.json b/sub-06/ses-017/anat/sub-06_ses-017_acq-axial_localizer.json new file mode 100644 index 000000000..a0733e062 --- /dev/null +++ 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"http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.998428, -0.0492981, 0.0266542, 0.0552964, 0.943927, -0.325491], + "ImageOrientationText": "Tra>Cor(-19.1)>Sag(0.5)", + "ImagingFrequency": 123.26, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": 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"TxRefAmp": 261.554, + "dcmmeta_affine": [ + [-1.9968568086624146, 0.1105927973985672, 0.018227169290184975, 100.59275817871094], + [0.09859614819288254, 1.887853741645813, -0.6529065370559692, -70.2121353149414], + [0.05330849438905716, 0.6509818434715271, 1.8903387784957886, -64.48714447021484], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From cd54105d1685714bb7405c4fb9f3ab7cac88222a Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:31:48 -0400 Subject: [PATCH 433/463] fix fmap phase --- ...6_ses-017_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-017_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-017_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-017_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-017_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - sub-06/ses-017/sub-06_ses-017_scans.tsv | 2 +- 21 files changed, 1 insertion(+), 791 deletions(-) rename sub-06/ses-017/fmap/{sub-06_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-06_ses-017_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-017/fmap/{sub-06_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-017_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-017/fmap/{sub-06_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-06_ses-017_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-06/ses-017/fmap/{sub-06_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-06_ses-017_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-06/ses-017/fmap/{sub-06_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-06_ses-017_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-06/ses-017/fmap/{sub-06_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-06_ses-017_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-06/ses-017/fmap/{sub-06_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-06_ses-017_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-06/ses-017/fmap/{sub-06_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-06_ses-017_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-06/ses-017/fmap/{sub-06_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-06_ses-017_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-06/ses-017/fmap/{sub-06_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-06_ses-017_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 610dcf335..000000000 --- a/sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:24:58.187500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.998428, -0.0492981, 0.0266542, 0.0552964, 0.943927, -0.325491], - "ImageOrientationText": "Tra>Cor(-19.1)>Sag(0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0498681, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [620, -7285, -8818, 548, 36, -254, -51, -11], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.0975, 0.8825, 0.195, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685, 0, 0.785, 0.0975, 0.8825, 0.195, 0.98, 0.295, 1.0775, 0.3925, 1.175, 0.49, 1.275, 0.5875, 1.3725, 0.685, 0, 0.785, 0.0975, 0.8825, 0.195, 0.98, 0.295, 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{ - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99842839044867, -0.0492980753971, 0.02665424747046, 0.05529639878241, 0.94392688678927, -0.3254909225739], - "ImagePositionPatient": [-879.09546323889, -775.52657703839, 220.11708568619], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.260311, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "162307.563000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.04986812453995, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "162544.277000", - "SliceLocation": -37.113534026083, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 1.9999999793661, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "162307.488000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["162458.187500", "162459.677500", "162501.167500"], - "ContentTime": ["162544.279000", "162544.282000", "162544.285000"], - "InstanceCreationTime": ["162544.279000", "162544.282000", "162544.285000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4888.0, 4890.0, 4894.0], - "WindowWidth": [18722.0, 18714.0, 18714.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index c9476d62f..000000000 --- a/sub-06/ses-017/fmap/sub-06_ses-017_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/78/7X/MD5E-s3334248--70c2b70c6ead496d406fcd5734426bb1.nii.gz/MD5E-s3334248--70c2b70c6ead496d406fcd5734426bb1.nii.gz \ No newline at end of file diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index f5d3dde90..000000000 --- a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:24:47.757500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998428, - -0.0492981, - 0.0266542, - 0.0552964, - 0.943927, - -0.325491 - ], - "ImageOrientationText": "Tra>Cor(-19.1)>Sag(0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0498681, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 620, - -7285, - -8818, - 548, - 36, - -254, - -51, - -11 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": 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sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 3574a45ff..000000000 --- a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:26:7.565000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998428, - -0.0492981, - 0.0266542, - 0.0552964, - 0.943927, - -0.325491 - ], - "ImageOrientationText": "Tra>Cor(-19.1)>Sag(0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0625303, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 620, - -7285, - -8818, - 548, - 36, - -254, - -51, - -11 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 261.554, - "WipMemBlock": "c4c7ab6f-8fb5-4610-be17-242d0b37c993||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 813e71746..000000000 --- a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/xZ/kW/MD5E-s1103386--9dcfbfd6bbbaca67c8cda1365f4ad535.nii.gz/MD5E-s1103386--9dcfbfd6bbbaca67c8cda1365f4ad535.nii.gz \ No newline at end of file diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 26c6199e9..000000000 --- a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:34:29.645000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - 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"Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0625303, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 620, - -7285, - -8818, - 548, - 36, - -254, - -51, - -11 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 261.554, - "WipMemBlock": "58ea3f7e-919c-4d1e-9148-bf084303d07d||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index c9b63e33f..000000000 --- a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/5V/Z1/MD5E-s1103523--c0c87445beff9d0bd62732c898afd502.nii.gz/MD5E-s1103523--c0c87445beff9d0bd62732c898afd502.nii.gz \ No newline at end of file diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index f1d8fb16d..000000000 --- a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "16:44:39.037500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998428, - -0.0492981, - 0.0266542, - 0.0552964, - 0.943927, - -0.325491 - ], - "ImageOrientationText": "Tra>Cor(-19.1)>Sag(0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.26, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0625303, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 620, - -7285, - -8818, - 548, - 36, - -254, - -51, - -11 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 261.554, - "WipMemBlock": "376c8bbb-77de-4d7b-9660-a7a814dabd1e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 9eb831bc0..000000000 --- a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/5k/Fv/MD5E-s1103523--2652d8168462aba410de19b7cefd2799.nii.gz/MD5E-s1103523--2652d8168462aba410de19b7cefd2799.nii.gz \ No newline at end of file diff --git a/sub-06/ses-017/sub-06_ses-017_scans.tsv b/sub-06/ses-017/sub-06_ses-017_scans.tsv index f82846169..908e62136 120000 --- a/sub-06/ses-017/sub-06_ses-017_scans.tsv +++ b/sub-06/ses-017/sub-06_ses-017_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/MF/mJ/MD5E-s2699--3a13cfcc4a87a3c427e0ab22081b8946.tsv/MD5E-s2699--3a13cfcc4a87a3c427e0ab22081b8946.tsv \ No newline at end of file +../../.git/annex/objects/zW/5F/MD5E-s2098--7b284d5934df77bdaf732b7d10f9fd48.tsv/MD5E-s2098--7b284d5934df77bdaf732b7d10f9fd48.tsv \ No newline at end of file From fd363617fc808ee09220827c8866e9f3481df594 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:31:57 -0400 Subject: [PATCH 434/463] fix complex event files --- ...g_events.tsv => sub-06_ses-017_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-06_ses-017_task-mario3_run-02_events.tsv} | 0 .../func/sub-06_ses-017_task-mario3_run-02_part-mag_events.tsv | 1 - .../func/sub-06_ses-017_task-mario3_run-02_part-phase_events.tsv | 1 - 4 files changed, 2 deletions(-) rename sub-06/ses-017/func/{sub-06_ses-017_task-mario3_run-01_part-mag_events.tsv => sub-06_ses-017_task-mario3_run-01_events.tsv} (100%) rename sub-06/ses-017/func/{sub-06_ses-017_task-mario3_run-01_part-phase_events.tsv => sub-06_ses-017_task-mario3_run-02_events.tsv} (100%) delete mode 120000 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-02_part-mag_events.tsv delete mode 120000 sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-02_part-phase_events.tsv diff --git a/sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_part-mag_events.tsv b/sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_events.tsv similarity index 100% rename from sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_part-mag_events.tsv rename to sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_events.tsv diff --git a/sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_part-phase_events.tsv b/sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-02_events.tsv similarity index 100% rename from sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-01_part-phase_events.tsv rename to sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-02_events.tsv diff --git a/sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-02_part-mag_events.tsv b/sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-02_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-02_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-02_part-phase_events.tsv b/sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-02_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-06/ses-017/func/sub-06_ses-017_task-mario3_run-02_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From c46f95d8e6d04f294291e5bedeee490dee733b6c Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:32:06 -0400 Subject: [PATCH 435/463] fill IntendedFor --- ...6_ses-017_acq-sbref_dir-AP_run-01_epi.json | 89 ++----------------- ...6_ses-017_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...6_ses-017_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- 3 files changed, 22 insertions(+), 243 deletions(-) diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_epi.json b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_epi.json index 0a75a7476..b6748618f 100644 --- a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998428, - -0.0492981, - 0.0266542, - 0.0552964, - 0.943927, - -0.325491 - ], + "ImageOrientationPatientDICOM": [0.998428, -0.0492981, 0.0266542, 0.0552964, 0.943927, -0.325491], "ImageOrientationText": "Tra>Cor(-19.1)>Sag(0.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,16 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-06_ses-017_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-017/func/sub-06_ses-017_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +64,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 620, - -7285, - -8818, - 548, - 36, - -254, - -51, - -11 - ], + "ShimSetting": [620, -7285, -8818, 548, 36, -254, -51, -11], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_epi.json b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_epi.json index 3dd01974b..736eacafa 100644 --- a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998428, - -0.0492981, - 0.0266542, - 0.0552964, - 0.943927, - -0.325491 - ], + "ImageOrientationPatientDICOM": [0.998428, -0.0492981, 0.0266542, 0.0552964, 0.943927, -0.325491], "ImageOrientationText": "Tra>Cor(-19.1)>Sag(0.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-06_ses-017_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 620, - -7285, - -8818, - 548, - 36, - -254, - -51, - -11 - ], + "ShimSetting": [620, -7285, -8818, 548, 36, -254, -51, -11], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_epi.json b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_epi.json index cdb776b9a..cdfbd09c3 100644 --- a/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-06/ses-017/fmap/sub-06_ses-017_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.998428, - -0.0492981, - 0.0266542, - 0.0552964, - 0.943927, - -0.325491 - ], + "ImageOrientationPatientDICOM": [0.998428, -0.0492981, 0.0266542, 0.0552964, 0.943927, -0.325491], "ImageOrientationText": "Tra>Cor(-19.1)>Sag(0.5)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.26, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-017/func/sub-06_ses-017_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 620, - -7285, - -8818, - 548, - 36, - -254, - -51, - -11 - ], + "ShimSetting": [620, -7285, -8818, 548, 36, -254, -51, -11], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 0502d1d50417e0c5dc1628fafc7a9350c878db40 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:36:47 -0400 Subject: [PATCH 436/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..938cc1c92 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = a8dd4cb6-82f2-4080-827c-3bd6fcd588d1 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..c95ad78bb --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit c95ad78bb1e6a9193348b536b72d609473e35506 From 8d7642988c436d6a8018a7bedb0069ba4fc3842c Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:37:19 -0400 Subject: [PATCH 437/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-05_ses-008_acq-axial_localizer.json | 81 +++ .../sub-05_ses-008_acq-axial_localizer.nii.gz | 1 + .../sub-05_ses-008_acq-coronal_localizer.json | 81 +++ ...ub-05_ses-008_acq-coronal_localizer.nii.gz | 1 + ...sub-05_ses-008_acq-sagittal_localizer.json | 86 +++ ...b-05_ses-008_acq-sagittal_localizer.nii.gz | 1 + sub-05/ses-008/anat/sub-05_ses-008_scout.json | 542 ++++++++++++++++++ .../ses-008/anat/sub-05_ses-008_scout.nii.gz | 1 + ...8_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-06_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-06_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 + ...-008_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-01_part-mag_events.tsv | 1 + ...008_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-01_part-phase_events.tsv | 1 + ...8_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-008_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-02_part-mag_events.tsv | 1 + ...008_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-02_part-phase_events.tsv | 1 + ...8_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-008_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-03_part-mag_events.tsv | 1 + ...008_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-03_part-phase_events.tsv | 1 + ...8_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-008_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-04_part-mag_events.tsv | 1 + ...008_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-04_part-phase_events.tsv | 1 + ...8_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-008_task-mario3_run-05_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-05_part-mag_events.tsv | 1 + ...008_task-mario3_run-05_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-05_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-05_part-phase_events.tsv | 1 + ...8_task-mario3_run-05_part-phase_sbref.json | 153 +++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + ...-008_task-mario3_run-06_part-mag_bold.json | 172 ++++++ ...08_task-mario3_run-06_part-mag_bold.nii.gz | 1 + ...008_task-mario3_run-06_part-mag_events.tsv | 1 + ...008_task-mario3_run-06_part-mag_sbref.json | 150 +++++ ...8_task-mario3_run-06_part-mag_sbref.nii.gz | 1 + ...08_task-mario3_run-06_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-06_part-phase_bold.nii.gz | 1 + ...8_task-mario3_run-06_part-phase_events.tsv | 1 + ...8_task-mario3_run-06_part-phase_sbref.json | 153 +++++ ...task-mario3_run-06_part-phase_sbref.nii.gz | 1 + sub-05/ses-008/sub-05_ses-008_scans.tsv | 1 + task-mario3_bold.json | 75 +++ 107 files changed, 7333 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-05/ses-008/anat/sub-05_ses-008_acq-axial_localizer.json create mode 120000 sub-05/ses-008/anat/sub-05_ses-008_acq-axial_localizer.nii.gz create mode 100644 sub-05/ses-008/anat/sub-05_ses-008_acq-coronal_localizer.json create mode 120000 sub-05/ses-008/anat/sub-05_ses-008_acq-coronal_localizer.nii.gz create mode 100644 sub-05/ses-008/anat/sub-05_ses-008_acq-sagittal_localizer.json create mode 120000 sub-05/ses-008/anat/sub-05_ses-008_acq-sagittal_localizer.nii.gz create mode 100644 sub-05/ses-008/anat/sub-05_ses-008_scout.json create mode 120000 sub-05/ses-008/anat/sub-05_ses-008_scout.nii.gz create mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.json create mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json create mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json create mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz create mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json create mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz create mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json create mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz create mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json create mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz create mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json create mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz create mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json create mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz create mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.json create mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz create mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.json create mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz create mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_part-mag_epi.json create mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz create mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_part-phase_epi.json create mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz create mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_part-mag_epi.json create mode 120000 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file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..da8d4ae9f --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-05 50 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-05/ses-008/anat/sub-05_ses-008_acq-axial_localizer.json b/sub-05/ses-008/anat/sub-05_ses-008_acq-axial_localizer.json new file mode 100644 index 000000000..c5b99dbd3 --- /dev/null +++ b/sub-05/ses-008/anat/sub-05_ses-008_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:46:53.162500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": 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+../../../.git/annex/objects/41/z7/MD5E-s178651--72380f316146a92104d436c40aee623b.nii.gz/MD5E-s178651--72380f316146a92104d436c40aee623b.nii.gz \ No newline at end of file diff --git a/sub-05/ses-008/anat/sub-05_ses-008_acq-coronal_localizer.json b/sub-05/ses-008/anat/sub-05_ses-008_acq-coronal_localizer.json new file mode 100644 index 000000000..1ae58180c --- /dev/null +++ b/sub-05/ses-008/anat/sub-05_ses-008_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:47:0.152500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, 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"SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "TxRefAmp": 289.133, + "dcmmeta_affine": [ + [-1.9992461204528809, 0.03908564895391464, 0.038562316447496414, 100.82984161376953], + [0.022997811436653137, 1.871599793434143, -0.7046880722045898, -71.35917663574219], + [0.049858205020427704, 0.7039790153503418, 1.8713438510894775, -57.700199127197266], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 7298727e06b6b778de83f4bbe2fc63bda9742078 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:37:58 -0400 Subject: [PATCH 438/463] fix fmap phase --- ...5_ses-008_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-008_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-008_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - ..._ses-008_acq-sbref_dir-PA_run-06_epi.json} | 0 ...es-008_acq-sbref_dir-PA_run-06_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 - sub-05/ses-008/sub-05_ses-008_scans.tsv | 2 +- 33 files changed, 1 insertion(+), 1250 deletions(-) rename sub-05/ses-008/fmap/{sub-05_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-05_ses-008_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-008/fmap/{sub-05_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-008_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-008/fmap/{sub-05_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-05_ses-008_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-008/fmap/{sub-05_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-008_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-008/fmap/{sub-05_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-05_ses-008_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-05/ses-008/fmap/{sub-05_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-05_ses-008_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-05/ses-008/fmap/{sub-05_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-05_ses-008_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-05/ses-008/fmap/{sub-05_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-05_ses-008_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-05/ses-008/fmap/{sub-05_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-05_ses-008_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-05/ses-008/fmap/{sub-05_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-05_ses-008_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-05/ses-008/fmap/{sub-05_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-05_ses-008_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-05/ses-008/fmap/{sub-05_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-05_ses-008_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-05/ses-008/fmap/{sub-05_ses-008_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-05_ses-008_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-05/ses-008/fmap/{sub-05_ses-008_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-05_ses-008_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz rename sub-05/ses-008/fmap/{sub-05_ses-008_acq-sbref_dir-PA_run-06_part-mag_epi.json => sub-05_ses-008_acq-sbref_dir-PA_run-06_epi.json} (100%) rename sub-05/ses-008/fmap/{sub-05_ses-008_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz => sub-05_ses-008_acq-sbref_dir-PA_run-06_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_part-phase_epi.json delete mode 120000 sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index b7a87e981..000000000 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:48:25.997500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.999623, -0.0114989, 0.0249291, 0.0195428, 0.9358, -0.35199], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0578474, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "ShimSetting": [595, -7294, -8797, 410, 31, -346, -40, 63], - "SliceThickness": 2, - "SliceTiming": [0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875, 0, 0.785, 0.0975, 0.8825, 0.1975, 0.98, 0.295, 1.0775, 0.3925, 1.1775, 0.49, 1.275, 0.5875, 1.3725, 0.6875], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 289.133, - "WipMemBlock": "25cd90ae-d600-454b-9e33-9c2c0b0daee0||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9992461204528809, 0.03908564895391464, 0.038562316447496414, 100.82984161376953], - [0.022997811436653137, 1.871599793434143, -0.7046880722045898, -71.35917663574219], - [0.049858205020427704, 0.7039790153503418, 1.8713438510894775, -57.700199127197266], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 3], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99962308647452, -0.0114989061639, 0.02492910235416, 0.0195428238097, 0.93579990477246, -0.3519895115843], - "ImagePositionPatient": [-846.80844885549, -794.30672849549, 252.90961723001], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - "ImagingFrequency": 123.258974, - "InPlanePhaseEncodingDirection": "COL", - "LargestImagePixelValue": 4095, - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3.0, - "Manufacturer": "SIEMENS", - "ManufacturerModelName": "Prisma_fit", - "Modality": "MR", - "NumberOfAverages": 1.0, - "NumberOfPhaseEncodingSteps": 104, - "PercentPhaseFieldOfView": 100.0, - "PercentSampling": 100.0, - "PerformedProcedureStepStartTime": "183831.130000", - "PhotometricInterpretation": "MONOCHROME2", - "PixelBandwidth": 2290.0, - "PixelRepresentation": 0, - "PixelSpacing": [2.0, 2.0], - "ProtocolName": "func_AP_run-1", - "RepetitionTime": 1490.0, - "RescaleIntercept": -4096.0, - "RescaleSlope": 2.0, - "RescaleType": "US", - "Rows": 832, - "SAR": 0.05784740507996, - "SamplesPerPixel": 1, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": [ - "SK", - "SS" -], - "SeriesDescription": "func_AP_run-1", - "SeriesNumber": 8, - "SeriesTime": "184912.946000", - "SliceLocation": -26.901359889195, - "SliceThickness": 2.0, - "SmallestImagePixelValue": 0, - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2.0000000181618, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "183831.060000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["184825.997500", "184827.487500", "184828.977500"], - "ContentTime": ["184912.948000", "184912.951000", "184912.954000"], - "InstanceCreationTime": ["184912.948000", "184912.951000", "184912.954000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4900.0, 4904.0, 4902.0], - "WindowWidth": [18710.0, 18712.0, 18712.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz b/sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 4d78f12e6..000000000 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/M5/xM/MD5E-s3334225--be407d99ed2050d2b1134ce50f471468.nii.gz/MD5E-s3334225--be407d99ed2050d2b1134ce50f471468.nii.gz \ No newline at end of file diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 1a5faa0c9..000000000 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:48:15.567500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999623, - -0.0114989, - 0.0249291, - 0.0195428, - 0.9358, - -0.35199 - ], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0578474, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 595, - -7294, - -8797, - 410, - 31, - -346, - -40, - 63 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 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-../../../.git/annex/objects/kQ/G4/MD5E-s1112152--bf4510d09fdb00aa0f5b232b8af7cfab.nii.gz/MD5E-s1112152--bf4510d09fdb00aa0f5b232b8af7cfab.nii.gz \ No newline at end of file diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index f8f3377ea..000000000 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:49:44.135000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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"%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0725356, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 595, - -7294, - -8797, - 410, - 31, - -346, - -40, - 63 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 289.133, - "WipMemBlock": "82fd9f3b-71fb-4cf4-a81b-8e52799c1ab8||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index fe11d863a..000000000 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/wm/XQ/MD5E-s1103473--9c60f990b4eb892c5c0d95c83b74dab5.nii.gz/MD5E-s1103473--9c60f990b4eb892c5c0d95c83b74dab5.nii.gz \ No newline at end of file diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index f87f76614..000000000 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:01:30.975000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999623, - -0.0114989, - 0.0249291, - 0.0195428, - 0.9358, - -0.35199 - ], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0725356, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 595, - -7294, - -8797, - 410, - 31, - -346, - -40, - 63 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 289.133, - "WipMemBlock": "d98716cb-b594-4a1c-82bd-ae8e9e42ab52||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index a70d6b0ea..000000000 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/F3/k8/MD5E-s1103590--b14e349123f8bb312d390f9169b0ec94.nii.gz/MD5E-s1103590--b14e349123f8bb312d390f9169b0ec94.nii.gz \ No newline at end of file diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 190521971..000000000 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:12:18.857500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of 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"MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0725356, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 595, - -7294, - -8797, - 410, - 31, - -346, - -40, - 63 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 289.133, - "WipMemBlock": "66330a21-be24-419d-b85a-24f23665e257||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 245b90e72..000000000 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/2k/7v/MD5E-s1103576--cdd4373c5a9b6c7c7c508b8cbc3368f9.nii.gz/MD5E-s1103576--cdd4373c5a9b6c7c7c508b8cbc3368f9.nii.gz \ No newline at end of file diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 67a9ae921..000000000 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:28:56.812500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999623, - -0.0114989, - 0.0249291, - 0.0195428, - 0.9358, - -0.35199 - ], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0725356, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 595, - -7294, - -8797, - 410, - 31, - -346, - -40, - 63 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 289.133, - "WipMemBlock": "b37ebf03-b2eb-49d0-a141-455110252fe5||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index f99ac9a6e..000000000 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/QM/7x/MD5E-s1103326--23a3de6c279c9e9e69739edccc5b516a.nii.gz/MD5E-s1103326--23a3de6c279c9e9e69739edccc5b516a.nii.gz \ No newline at end of file diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index 3ca472c2d..000000000 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:38:52.667500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999623, - -0.0114989, - 0.0249291, - 0.0195428, - 0.9358, - -0.35199 - ], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-05", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0725356, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 595, - -7294, - -8797, - 410, - 31, - -346, - -40, - 63 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 289.133, - "WipMemBlock": "262bf01d-8ebf-4042-9a2c-39610687954e||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index a156b19da..000000000 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Jv/KP/MD5E-s1103347--9ecbef67dab6911b5ea5e647e2e6a2a3.nii.gz/MD5E-s1103347--9ecbef67dab6911b5ea5e647e2e6a2a3.nii.gz \ No newline at end of file diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_part-mag_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_epi.json similarity index 100% rename from sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_part-mag_epi.json rename to sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_epi.json diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_epi.nii.gz similarity index 100% rename from sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz rename to sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_epi.nii.gz diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_part-phase_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_part-phase_epi.json deleted file mode 100644 index 42ae4ae47..000000000 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:48:42.785000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999623, - -0.0114989, - 0.0249291, - 0.0195428, - 0.9358, - -0.35199 - ], - "ImageOrientationText": "Tra>Cor(-20.6)>Sag(1.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-06", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0725356, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-06_SBRef", - "SeriesNumber": 24, - "ShimSetting": [ - 595, - -7294, - -8797, - 410, - 31, - -346, - -40, - 63 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.995, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 289.133, - "WipMemBlock": "7ac32722-2b61-4e1f-b56d-4402207177e5||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz deleted file mode 120000 index a20306941..000000000 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/ZJ/Zw/MD5E-s1103454--b01b312b709994d0089be5dc418882f4.nii.gz/MD5E-s1103454--b01b312b709994d0089be5dc418882f4.nii.gz \ No newline at end of file diff --git a/sub-05/ses-008/sub-05_ses-008_scans.tsv b/sub-05/ses-008/sub-05_ses-008_scans.tsv index e59394373..5d8e0d881 120000 --- a/sub-05/ses-008/sub-05_ses-008_scans.tsv +++ b/sub-05/ses-008/sub-05_ses-008_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/F3/9G/MD5E-s4533--1c919f92cda5a08381aec4751f215b64.tsv/MD5E-s4533--1c919f92cda5a08381aec4751f215b64.tsv \ No newline at end of file +../../.git/annex/objects/1p/w4/MD5E-s3569--3751f95d711c17fee2449a8e12e2c19c.tsv/MD5E-s3569--3751f95d711c17fee2449a8e12e2c19c.tsv \ No newline at end of file From 9d6ae23864a5301628b4f0505e043f3f4ccaf633 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:38:10 -0400 Subject: [PATCH 439/463] fix complex event files --- ...g_events.tsv => sub-05_ses-008_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-05_ses-008_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-05_ses-008_task-mario3_run-03_events.tsv} | 0 ...e_events.tsv => sub-05_ses-008_task-mario3_run-04_events.tsv} | 0 .../func/sub-05_ses-008_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-05_ses-008_task-mario3_run-04_part-phase_events.tsv | 1 - ...g_events.tsv => sub-05_ses-008_task-mario3_run-05_events.tsv} | 0 .../func/sub-05_ses-008_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-05_ses-008_task-mario3_run-05_part-phase_events.tsv | 1 - ...e_events.tsv => sub-05_ses-008_task-mario3_run-06_events.tsv} | 0 .../func/sub-05_ses-008_task-mario3_run-06_part-mag_events.tsv | 1 - .../func/sub-05_ses-008_task-mario3_run-06_part-phase_events.tsv | 1 - 12 files changed, 6 deletions(-) rename sub-05/ses-008/func/{sub-05_ses-008_task-mario3_run-01_part-mag_events.tsv => sub-05_ses-008_task-mario3_run-01_events.tsv} (100%) rename sub-05/ses-008/func/{sub-05_ses-008_task-mario3_run-01_part-phase_events.tsv => sub-05_ses-008_task-mario3_run-02_events.tsv} (100%) rename sub-05/ses-008/func/{sub-05_ses-008_task-mario3_run-02_part-mag_events.tsv => sub-05_ses-008_task-mario3_run-03_events.tsv} (100%) rename sub-05/ses-008/func/{sub-05_ses-008_task-mario3_run-02_part-phase_events.tsv => sub-05_ses-008_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-04_part-phase_events.tsv rename sub-05/ses-008/func/{sub-05_ses-008_task-mario3_run-03_part-mag_events.tsv => sub-05_ses-008_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-05_part-phase_events.tsv rename sub-05/ses-008/func/{sub-05_ses-008_task-mario3_run-03_part-phase_events.tsv => sub-05_ses-008_task-mario3_run-06_events.tsv} (100%) delete mode 120000 sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-06_part-mag_events.tsv delete mode 120000 sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-06_part-phase_events.tsv diff --git a/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-01_part-mag_events.tsv b/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-01_events.tsv similarity index 100% rename from sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-01_part-mag_events.tsv rename to sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-01_events.tsv diff --git a/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-01_part-phase_events.tsv b/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-02_events.tsv similarity index 100% rename from sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-01_part-phase_events.tsv rename to sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-02_events.tsv diff --git a/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-02_part-mag_events.tsv b/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-03_events.tsv similarity index 100% rename from sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-02_part-mag_events.tsv rename to sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-03_events.tsv diff --git a/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-02_part-phase_events.tsv b/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-04_events.tsv similarity index 100% rename from sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-02_part-phase_events.tsv rename to sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-04_events.tsv diff --git a/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-04_part-mag_events.tsv b/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-04_part-phase_events.tsv b/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-03_part-mag_events.tsv b/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-05_events.tsv similarity index 100% rename from sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-03_part-mag_events.tsv rename to sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-05_events.tsv diff --git a/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-05_part-mag_events.tsv b/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-05_part-phase_events.tsv b/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-03_part-phase_events.tsv b/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-06_events.tsv similarity index 100% rename from sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-03_part-phase_events.tsv rename to sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-06_events.tsv diff --git a/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-06_part-mag_events.tsv b/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-06_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-06_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-06_part-phase_events.tsv b/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-06_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-008/func/sub-05_ses-008_task-mario3_run-06_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 13fcd04a5b3d4f92b3d309a04eb8a8c0873b2fce Mon Sep 17 00:00:00 2001 From: test Date: Fri, 26 May 2023 11:38:21 -0400 Subject: [PATCH 440/463] fill IntendedFor --- ...5_ses-008_acq-sbref_dir-AP_run-01_epi.json | 93 +++---------------- ...5_ses-008_acq-sbref_dir-PA_run-01_epi.json | 88 ++---------------- ...5_ses-008_acq-sbref_dir-PA_run-02_epi.json | 88 ++---------------- ...5_ses-008_acq-sbref_dir-PA_run-03_epi.json | 88 ++---------------- ...5_ses-008_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- ...5_ses-008_acq-sbref_dir-PA_run-05_epi.json | 88 ++---------------- ...5_ses-008_acq-sbref_dir-PA_run-06_epi.json | 88 ++---------------- 7 files changed, 54 insertions(+), 567 deletions(-) diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_epi.json index 8e6697bbc..9138bcb69 100644 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999623, - -0.0114989, - 0.0249291, - 0.0195428, - 0.9358, - -0.35199 - ], + "ImageOrientationPatientDICOM": [0.999623, -0.0114989, 0.0249291, 0.0195428, 0.9358, -0.35199], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,20 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-05_ses-008_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-008/func/sub-05_ses-008_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-008/func/sub-05_ses-008_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-008/func/sub-05_ses-008_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-008/func/sub-05_ses-008_task-mario3_run-05_part-mag_bold.nii.gz", + "ses-008/func/sub-05_ses-008_task-mario3_run-06_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +68,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 595, - -7294, - -8797, - 410, - 31, - -346, - -40, - 63 - ], + "ShimSetting": [595, -7294, -8797, 410, 31, -346, -40, 63], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_epi.json index 6229c32ce..30a6ccaf3 100644 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999623, - -0.0114989, - 0.0249291, - 0.0195428, - 0.9358, - -0.35199 - ], + "ImageOrientationPatientDICOM": [0.999623, -0.0114989, 0.0249291, 0.0195428, 0.9358, -0.35199], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-05_ses-008_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 595, - -7294, - -8797, - 410, - 31, - -346, - -40, - 63 - ], + "ShimSetting": [595, -7294, -8797, 410, 31, -346, -40, 63], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_epi.json index 592c2b0df..ecb67f55d 100644 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999623, - -0.0114989, - 0.0249291, - 0.0195428, - 0.9358, - -0.35199 - ], + "ImageOrientationPatientDICOM": [0.999623, -0.0114989, 0.0249291, 0.0195428, 0.9358, -0.35199], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-05_ses-008_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 595, - -7294, - -8797, - 410, - 31, - -346, - -40, - 63 - ], + "ShimSetting": [595, -7294, -8797, 410, 31, -346, -40, 63], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_epi.json index d0fb69e13..315492a52 100644 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999623, - -0.0114989, - 0.0249291, - 0.0195428, - 0.9358, - -0.35199 - ], + "ImageOrientationPatientDICOM": [0.999623, -0.0114989, 0.0249291, 0.0195428, 0.9358, -0.35199], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-05_ses-008_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 595, - -7294, - -8797, - 410, - 31, - -346, - -40, - 63 - ], + "ShimSetting": [595, -7294, -8797, 410, 31, -346, -40, 63], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_epi.json index f5feabac6..504634309 100644 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999623, - -0.0114989, - 0.0249291, - 0.0195428, - 0.9358, - -0.35199 - ], + "ImageOrientationPatientDICOM": [0.999623, -0.0114989, 0.0249291, 0.0195428, 0.9358, -0.35199], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-05_ses-008_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 595, - -7294, - -8797, - 410, - 31, - -346, - -40, - 63 - ], + "ShimSetting": [595, -7294, -8797, 410, 31, -346, -40, 63], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_epi.json index 457a97f61..31e7406f5 100644 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999623, - -0.0114989, - 0.0249291, - 0.0195428, - 0.9358, - -0.35199 - ], + "ImageOrientationPatientDICOM": [0.999623, -0.0114989, 0.0249291, 0.0195428, 0.9358, -0.35199], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-05_ses-008_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 595, - -7294, - -8797, - 410, - 31, - -346, - -40, - 63 - ], + "ShimSetting": [595, -7294, -8797, 410, 31, -346, -40, 63], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.3125, 4.41, 4.5075, 4.605, 4.7025, 4.8025, 4.9, 4.9975, 5.095, 5.1925, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_epi.json b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_epi.json index 47235a7d1..af11cd995 100644 --- a/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_epi.json +++ b/sub-05/ses-008/fmap/sub-05_ses-008_acq-sbref_dir-PA_run-06_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999623, - -0.0114989, - 0.0249291, - 0.0195428, - 0.9358, - -0.35199 - ], + "ImageOrientationPatientDICOM": [0.999623, -0.0114989, 0.0249291, 0.0195428, 0.9358, -0.35199], "ImageOrientationText": "Tra>Cor(-20.6)>Sag(1.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-008/func/sub-05_ses-008_task-mario3_run-06_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-06_SBRef", "SeriesNumber": 24, - "ShimSetting": [ - 595, - -7294, - -8797, - 410, - 31, - -346, - -40, - 63 - ], + "ShimSetting": [595, -7294, -8797, 410, 31, -346, -40, 63], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.995, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.4875, 0.5875, 0.685, 0.7825, 0.88, 0.9775, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.995, 5.095, 5.1925, 5.29, 5.3875, 5.485, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From cc9ba4a0eba39b1ac7dca367774be2023b2bdf61 Mon Sep 17 00:00:00 2001 From: test Date: Tue, 29 Aug 2023 15:31:04 -0400 Subject: [PATCH 441/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..858ea0a06 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 533a7eaa-7ab9-41dc-b135-4a0617baa850 diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..4c6ff8f9c --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 4c6ff8f9c32cb233680a39ee13ce643b33fb523e From 63ce3cca695f89e1fd06cf014ec3b3bf536a5ddc Mon Sep 17 00:00:00 2001 From: test Date: Tue, 29 Aug 2023 15:31:38 -0400 Subject: [PATCH 442/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-05_ses-009_acq-axial_localizer.json | 81 +++ .../sub-05_ses-009_acq-axial_localizer.nii.gz | 1 + ...5_ses-009_acq-axial_localizer__dup-01.json | 81 +++ ...ses-009_acq-axial_localizer__dup-01.nii.gz | 1 + .../sub-05_ses-009_acq-coronal_localizer.json | 81 +++ ...ub-05_ses-009_acq-coronal_localizer.nii.gz | 1 + ...ses-009_acq-coronal_localizer__dup-01.json | 81 +++ ...s-009_acq-coronal_localizer__dup-01.nii.gz | 1 + ...sub-05_ses-009_acq-sagittal_localizer.json | 86 +++ ...b-05_ses-009_acq-sagittal_localizer.nii.gz | 1 + ...es-009_acq-sagittal_localizer__dup-01.json | 86 +++ ...-009_acq-sagittal_localizer__dup-01.nii.gz | 1 + sub-05/ses-009/anat/sub-05_ses-009_scout.json | 542 ++++++++++++++++++ .../ses-009/anat/sub-05_ses-009_scout.nii.gz | 1 + .../anat/sub-05_ses-009_scout__dup-01.json | 542 ++++++++++++++++++ .../anat/sub-05_ses-009_scout__dup-01.nii.gz | 1 + ...9_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...ld_dir-AP_run-01_part-mag_epi__dup-01.json | 171 ++++++ ..._dir-AP_run-01_part-mag_epi__dup-01.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._dir-AP_run-01_part-phase_epi__dup-01.json | 177 ++++++ ...ir-AP_run-01_part-phase_epi__dup-01.nii.gz | 1 + ...ef_dir-AP_run-01_epi__part-mag_dup-01.json | 149 +++++ ..._dir-AP_run-01_epi__part-mag_dup-01.nii.gz | 1 + ..._dir-AP_run-01_epi__part-phase_dup-01.json | 152 +++++ ...ir-AP_run-01_epi__part-phase_dup-01.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-06_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-06_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 + ...-009_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...09_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...009_task-mario3_run-01_part-mag_events.tsv | 1 + ...009_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...09_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-01_part-phase_events.tsv | 1 + ...9_task-mario3_run-01_part-phase_sbref.json | 153 +++++ ...task-mario3_run-01_part-phase_sbref.nii.gz | 1 + ...-009_task-mario3_run-02_part-mag_bold.json | 172 ++++++ ...09_task-mario3_run-02_part-mag_bold.nii.gz | 1 + ...009_task-mario3_run-02_part-mag_events.tsv | 1 + ...009_task-mario3_run-02_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-02_part-mag_sbref.nii.gz | 1 + ...09_task-mario3_run-02_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-02_part-phase_events.tsv | 1 + ...9_task-mario3_run-02_part-phase_sbref.json | 153 +++++ ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 + ...-009_task-mario3_run-03_part-mag_bold.json | 172 ++++++ ...09_task-mario3_run-03_part-mag_bold.nii.gz | 1 + ...009_task-mario3_run-03_part-mag_events.tsv | 1 + ...009_task-mario3_run-03_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-03_part-mag_sbref.nii.gz | 1 + ...09_task-mario3_run-03_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-03_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-03_part-phase_events.tsv | 1 + ...9_task-mario3_run-03_part-phase_sbref.json | 153 +++++ ...task-mario3_run-03_part-phase_sbref.nii.gz | 1 + ...-009_task-mario3_run-04_part-mag_bold.json | 172 ++++++ ...09_task-mario3_run-04_part-mag_bold.nii.gz | 1 + ...009_task-mario3_run-04_part-mag_events.tsv | 1 + ...009_task-mario3_run-04_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-04_part-mag_sbref.nii.gz | 1 + ...09_task-mario3_run-04_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-04_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-04_part-phase_events.tsv | 1 + ...9_task-mario3_run-04_part-phase_sbref.json | 153 +++++ ...task-mario3_run-04_part-phase_sbref.nii.gz | 1 + ...-009_task-mario3_run-05_part-mag_bold.json | 172 ++++++ ...09_task-mario3_run-05_part-mag_bold.nii.gz | 1 + ...009_task-mario3_run-05_part-mag_events.tsv | 1 + ...009_task-mario3_run-05_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-05_part-mag_sbref.nii.gz | 1 + ...09_task-mario3_run-05_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-05_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-05_part-phase_events.tsv | 1 + ...9_task-mario3_run-05_part-phase_sbref.json | 153 +++++ ...task-mario3_run-05_part-phase_sbref.nii.gz | 1 + ...-009_task-mario3_run-06_part-mag_bold.json | 172 ++++++ ...09_task-mario3_run-06_part-mag_bold.nii.gz | 1 + ...009_task-mario3_run-06_part-mag_events.tsv | 1 + ...009_task-mario3_run-06_part-mag_sbref.json | 150 +++++ ...9_task-mario3_run-06_part-mag_sbref.nii.gz | 1 + ...09_task-mario3_run-06_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-06_part-phase_bold.nii.gz | 1 + ...9_task-mario3_run-06_part-phase_events.tsv | 1 + ...9_task-mario3_run-06_part-phase_sbref.json | 153 +++++ ...task-mario3_run-06_part-phase_sbref.nii.gz | 1 + sub-05/ses-009/sub-05_ses-009_scans.tsv | 1 + task-mario3_bold.json | 64 +++ 123 files changed, 8769 insertions(+), 1 deletion(-) create mode 100644 CHANGES create mode 100644 participants.json create mode 100644 participants.tsv create mode 100644 scans.json create mode 100644 sub-05/ses-009/anat/sub-05_ses-009_acq-axial_localizer.json create mode 120000 sub-05/ses-009/anat/sub-05_ses-009_acq-axial_localizer.nii.gz create mode 100644 sub-05/ses-009/anat/sub-05_ses-009_acq-axial_localizer__dup-01.json create mode 120000 sub-05/ses-009/anat/sub-05_ses-009_acq-axial_localizer__dup-01.nii.gz create mode 100644 sub-05/ses-009/anat/sub-05_ses-009_acq-coronal_localizer.json create mode 120000 sub-05/ses-009/anat/sub-05_ses-009_acq-coronal_localizer.nii.gz create mode 100644 sub-05/ses-009/anat/sub-05_ses-009_acq-coronal_localizer__dup-01.json create mode 120000 sub-05/ses-009/anat/sub-05_ses-009_acq-coronal_localizer__dup-01.nii.gz create mode 100644 sub-05/ses-009/anat/sub-05_ses-009_acq-sagittal_localizer.json create mode 120000 sub-05/ses-009/anat/sub-05_ses-009_acq-sagittal_localizer.nii.gz create mode 100644 sub-05/ses-009/anat/sub-05_ses-009_acq-sagittal_localizer__dup-01.json create mode 120000 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sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-phase_bold.json create mode 120000 sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-phase_bold.nii.gz create mode 120000 sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-phase_events.tsv create mode 100644 sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-phase_sbref.json create mode 120000 sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-phase_sbref.nii.gz create mode 120000 sub-05/ses-009/sub-05_ses-009_scans.tsv create mode 100644 task-mario3_bold.json diff --git a/.heudiconv b/.heudiconv index 4c6ff8f9c..2c6d1c2f3 160000 --- a/.heudiconv +++ b/.heudiconv @@ -1 +1 @@ -Subproject commit 4c6ff8f9c32cb233680a39ee13ce643b33fb523e +Subproject commit 2c6d1c2f3b61edc4b69e96c1b9b5c5dbd43190f3 diff --git a/CHANGES b/CHANGES new file mode 100644 index 000000000..061247385 --- /dev/null +++ b/CHANGES @@ -0,0 +1,5 @@ +0.0.1 Initial data acquired +TODOs: + - verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208) + - fill out dataset_description.json, README, sourcedata/README (if present) + - provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..da8d4ae9f --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-05 50 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-05/ses-009/anat/sub-05_ses-009_acq-axial_localizer.json b/sub-05/ses-009/anat/sub-05_ses-009_acq-axial_localizer.json new file mode 100644 index 000000000..2ea18eef9 --- /dev/null +++ b/sub-05/ses-009/anat/sub-05_ses-009_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "19:28:38.052500", + "BaseResolution": 256, + 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end of file diff --git a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-phase_events.tsv b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-phase_events.tsv new file mode 120000 index 000000000..1bbdfddb5 --- /dev/null +++ b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-phase_events.tsv @@ -0,0 +1 @@ +../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-phase_sbref.json b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-phase_sbref.json new file mode 100644 index 000000000..8d936efb4 --- /dev/null +++ b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-phase_sbref.json @@ -0,0 +1,153 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "19:51:12.710000", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + 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a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-phase_sbref.nii.gz b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-phase_sbref.nii.gz new file mode 120000 index 000000000..dcf22a832 --- /dev/null +++ b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/J7/F8/MD5E-s1103588--659a8fe023fa9f1f273d5ae6cdb3886e.nii.gz/MD5E-s1103588--659a8fe023fa9f1f273d5ae6cdb3886e.nii.gz \ No newline at end of file diff --git a/sub-05/ses-009/sub-05_ses-009_scans.tsv b/sub-05/ses-009/sub-05_ses-009_scans.tsv new file mode 120000 index 000000000..150e99c96 --- /dev/null +++ b/sub-05/ses-009/sub-05_ses-009_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/1w/f1/MD5E-s5362--f8ab31e89766f2f7786a090515290854.tsv/MD5E-s5362--f8ab31e89766f2f7786a090515290854.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..c2df6e4b1 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,64 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From a6f8158b49dba7f4c64d795d4a7a599de8ea0fe4 Mon Sep 17 00:00:00 2001 From: test Date: Tue, 29 Aug 2023 15:32:16 -0400 Subject: [PATCH 443/463] fix fmap phase --- ...5_ses-009_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-009_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...9_acq-bold_dir-AP_run-01_epi__dup-01.json} | 0 ...acq-bold_dir-AP_run-01_epi__dup-01.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._dir-AP_run-01_part-phase_epi__dup-01.json | 177 ------------------ ...ir-AP_run-01_part-phase_epi__dup-01.nii.gz | 1 - ..._ses-009_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-009_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ..._acq-sbref_dir-AP_run-01_epi__dup-01.json} | 0 ...cq-sbref_dir-AP_run-01_epi__dup-01.nii.gz} | 0 ..._dir-AP_run-01_epi__part-phase_dup-01.json | 152 --------------- ...ir-AP_run-01_epi__part-phase_dup-01.nii.gz | 1 - ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-009_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-009_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-009_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-009_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-009_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - ..._ses-009_acq-sbref_dir-PA_run-06_epi.json} | 0 ...es-009_acq-sbref_dir-PA_run-06_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 - sub-05/ses-009/sub-05_ses-009_scans.tsv | 2 +- 41 files changed, 1 insertion(+), 1581 deletions(-) rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-05_ses-009_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-009_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-bold_dir-AP_run-01_part-mag_epi__dup-01.json => sub-05_ses-009_acq-bold_dir-AP_run-01_epi__dup-01.json} (100%) rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-bold_dir-AP_run-01_part-mag_epi__dup-01.nii.gz => sub-05_ses-009_acq-bold_dir-AP_run-01_epi__dup-01.nii.gz} (100%) delete mode 100644 sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz delete mode 100644 sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-phase_epi__dup-01.json delete mode 120000 sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-phase_epi__dup-01.nii.gz rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-05_ses-009_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-009_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__part-mag_dup-01.json => sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__dup-01.json} (100%) rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__part-mag_dup-01.nii.gz => sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__dup-01.nii.gz} (100%) delete mode 100644 sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__part-phase_dup-01.json delete mode 120000 sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__part-phase_dup-01.nii.gz delete mode 100644 sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-05_ses-009_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-05_ses-009_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-05_ses-009_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-05_ses-009_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-05_ses-009_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-05_ses-009_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-05_ses-009_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-05_ses-009_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-05_ses-009_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-05_ses-009_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-sbref_dir-PA_run-06_part-mag_epi.json => sub-05_ses-009_acq-sbref_dir-PA_run-06_epi.json} (100%) rename sub-05/ses-009/fmap/{sub-05_ses-009_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz => sub-05_ses-009_acq-sbref_dir-PA_run-06_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_part-phase_epi.json delete mode 120000 sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-mag_epi__dup-01.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_epi__dup-01.json similarity index 100% rename from sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-mag_epi__dup-01.json rename to sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_epi__dup-01.json diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-mag_epi__dup-01.nii.gz b/sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_epi__dup-01.nii.gz similarity index 100% rename from sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-mag_epi__dup-01.nii.gz rename to sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_epi__dup-01.nii.gz diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index b651d3da7..000000000 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:29:38.170000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": 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+++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/K1/9w/MD5E-s3333704--6bccfff3de26ef9a4ef8d2ff278474cd.nii.gz/MD5E-s3333704--6bccfff3de26ef9a4ef8d2ff278474cd.nii.gz \ No newline at end of file diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-phase_epi__dup-01.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-phase_epi__dup-01.json deleted file mode 100644 index 13565e31d..000000000 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-phase_epi__dup-01.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:35:47.360000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - 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"N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3], - "AcquisitionTime": ["183547.360000", "183548.850000", "183550.340000"], - "ContentTime": ["183632.766000", "183632.768000", "183632.771000"], - "InstanceCreationTime": ["183632.766000", "183632.768000", "183632.771000"], - "InstanceNumber": [1, 2, 3], - "WindowCenter": [4868.0, 4864.0, 4874.0], - "WindowWidth": [18682.0, 18678.0, 18682.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-phase_epi__dup-01.nii.gz b/sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-phase_epi__dup-01.nii.gz deleted file mode 120000 index c3583a0e2..000000000 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-bold_dir-AP_run-01_part-phase_epi__dup-01.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/QW/8p/MD5E-s3334344--c284a63ec71f7fef0583630ef34d4855.nii.gz/MD5E-s3334344--c284a63ec71f7fef0583630ef34d4855.nii.gz \ No newline at end of file diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__part-mag_dup-01.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__dup-01.json similarity index 100% rename from sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__part-mag_dup-01.json rename to sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__dup-01.json diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__part-mag_dup-01.nii.gz b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__dup-01.nii.gz similarity index 100% rename from sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__part-mag_dup-01.nii.gz rename to sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__dup-01.nii.gz diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__part-phase_dup-01.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__part-phase_dup-01.json deleted file mode 100644 index db87cd857..000000000 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__part-phase_dup-01.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:35:36.930000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.9997, - -0.02448, - 0.000551984, - 0.0226864, - 0.917499, - -0.39709 - ], - "ImageOrientationText": "Tra>Cor(-23.4)>Sag(-0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0622177, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-1_SBRef", - "SeriesNumber": 6, - "ShimSetting": [ - 580, - -7304, - -8798, - 410, - 13, - -380, - -47, - 93 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 298.107, - "WipMemBlock": "b9202c80-3403-4cb8-b3bc-3d80b9ea5eff||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__part-phase_dup-01.nii.gz b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__part-phase_dup-01.nii.gz deleted file mode 120000 index 9e81612a4..000000000 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi__part-phase_dup-01.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/6M/2V/MD5E-s1112039--c694afbb48e88e855ad9c55e5af3c18a.nii.gz/MD5E-s1112039--c694afbb48e88e855ad9c55e5af3c18a.nii.gz \ No newline at end of file diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 3af138607..000000000 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:29:27.740000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999892, - -0.0123771, - 0.00797348, - 0.0144857, - 0.923873, - -0.382425 - ], - "ImageOrientationText": "Tra>Cor(-22.5)>Sag(0.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j-", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_AP_run-1", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0501952, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_AP_run-2_SBRef", - "SeriesNumber": 23, - "ShimSetting": [ - 587, - -7295, - -8817, - 401, - 21, - -370, - -75, - 95 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.51, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 274.908, - "WipMemBlock": "3a94e296-efdc-4039-b2a2-cd314587f945||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 219b849bb..000000000 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/9M/6q/MD5E-s1112115--5ff50f2c08c5b030f7ad1e52b2c34b8c.nii.gz/MD5E-s1112115--5ff50f2c08c5b030f7ad1e52b2c34b8c.nii.gz \ No newline at end of file diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index 9d4a51826..000000000 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:36:45.085000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.9997, - -0.02448, - 0.000551984, - 0.0226864, - 0.917499, - -0.39709 - ], - "ImageOrientationText": "Tra>Cor(-23.4)>Sag(-0.5)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-01", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0780156, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 580, - -7304, - -8798, - 410, - 13, - -379, - -47, - 94 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 298.107, - "WipMemBlock": "acdf2a41-f67a-4a97-870d-786d045cb669||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index 2abc4d3ad..000000000 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/wM/9f/MD5E-s1103654--3f1c843e8942820971fb5f1d16606523.nii.gz/MD5E-s1103654--3f1c843e8942820971fb5f1d16606523.nii.gz \ No newline at end of file diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 62b1b4e48..000000000 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:47:11.977500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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"PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-02", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0780156, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 580, - -7304, - -8798, - 410, - 13, - -379, - -47, - 94 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, 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b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 1e0763090..000000000 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:59:51.362500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index fb9cc0835..000000000 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:30:37.047500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999892, - -0.0123771, - 0.00797348, - 0.0144857, - 0.923873, - -0.382425 - ], - "ImageOrientationText": "Tra>Cor(-22.5)>Sag(0.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0629404, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 26, - "ShimSetting": [ - 588, - -7296, - -8818, - 399, - 23, - -371, - -74, - 95 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 274.908, - "WipMemBlock": "d3f10537-6cf7-4f1a-9083-d0f49e091a2d||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 7e8bf5288..000000000 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/J0/zJ/MD5E-s1103576--d69d5bae01f010743a71ce4af0c74c47.nii.gz/MD5E-s1103576--d69d5bae01f010743a71ce4af0c74c47.nii.gz \ No newline at end of file diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index 7d1a2d999..000000000 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:41:23.717500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999892, - -0.0123771, - 0.00797348, - 0.0144857, - 0.923873, - -0.382425 - ], - "ImageOrientationText": "Tra>Cor(-22.5)>Sag(0.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-05", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0629404, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 29, - "ShimSetting": [ - 588, - -7296, - -8818, - 399, - 23, - -371, - -74, - 95 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 274.908, - "WipMemBlock": "a5a8859a-a009-475f-905f-a053231526c1||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index 0dec415a8..000000000 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/zG/6F/MD5E-s1103647--dce6d598efe121a58b50d2fe07abf53a.nii.gz/MD5E-s1103647--dce6d598efe121a58b50d2fe07abf53a.nii.gz \ No newline at end of file diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_part-mag_epi.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_epi.json similarity index 100% rename from sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_part-mag_epi.json rename to sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_epi.json diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_epi.nii.gz similarity index 100% rename from sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz rename to sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_epi.nii.gz diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_part-phase_epi.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_part-phase_epi.json deleted file mode 100644 index 12aeaf467..000000000 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:51:12.710000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999892, - -0.0123771, - 0.00797348, - 0.0144857, - 0.923873, - -0.382425 - ], - "ImageOrientationText": "Tra>Cor(-22.5)>Sag(0.2)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-06", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0629404, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-06_SBRef", - "SeriesNumber": 32, - "ShimSetting": [ - 588, - -7296, - -8818, - 399, - 23, - -371, - -74, - 95 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 274.908, - "WipMemBlock": "131bf780-4962-425a-ab93-818b158f0f6a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz deleted file mode 120000 index dcf22a832..000000000 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/J7/F8/MD5E-s1103588--659a8fe023fa9f1f273d5ae6cdb3886e.nii.gz/MD5E-s1103588--659a8fe023fa9f1f273d5ae6cdb3886e.nii.gz \ No newline at end of file diff --git a/sub-05/ses-009/sub-05_ses-009_scans.tsv b/sub-05/ses-009/sub-05_ses-009_scans.tsv index 150e99c96..5b988db3a 120000 --- a/sub-05/ses-009/sub-05_ses-009_scans.tsv +++ b/sub-05/ses-009/sub-05_ses-009_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/1w/f1/MD5E-s5362--f8ab31e89766f2f7786a090515290854.tsv/MD5E-s5362--f8ab31e89766f2f7786a090515290854.tsv \ No newline at end of file +../../.git/annex/objects/VM/wM/MD5E-s4145--147ea5bd905ec6c242270aedd8954b89.tsv/MD5E-s4145--147ea5bd905ec6c242270aedd8954b89.tsv \ No newline at end of file From f8c55e311eadac9cc04e3a65644f52b4acf625b4 Mon Sep 17 00:00:00 2001 From: test Date: Tue, 29 Aug 2023 15:32:26 -0400 Subject: [PATCH 444/463] fix complex event files --- ...g_events.tsv => sub-05_ses-009_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-05_ses-009_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-05_ses-009_task-mario3_run-03_events.tsv} | 0 ...e_events.tsv => sub-05_ses-009_task-mario3_run-04_events.tsv} | 0 .../func/sub-05_ses-009_task-mario3_run-04_part-mag_events.tsv | 1 - .../func/sub-05_ses-009_task-mario3_run-04_part-phase_events.tsv | 1 - ...g_events.tsv => sub-05_ses-009_task-mario3_run-05_events.tsv} | 0 .../func/sub-05_ses-009_task-mario3_run-05_part-mag_events.tsv | 1 - .../func/sub-05_ses-009_task-mario3_run-05_part-phase_events.tsv | 1 - ...e_events.tsv => sub-05_ses-009_task-mario3_run-06_events.tsv} | 0 .../func/sub-05_ses-009_task-mario3_run-06_part-mag_events.tsv | 1 - .../func/sub-05_ses-009_task-mario3_run-06_part-phase_events.tsv | 1 - 12 files changed, 6 deletions(-) rename sub-05/ses-009/func/{sub-05_ses-009_task-mario3_run-01_part-mag_events.tsv => sub-05_ses-009_task-mario3_run-01_events.tsv} (100%) rename sub-05/ses-009/func/{sub-05_ses-009_task-mario3_run-01_part-phase_events.tsv => sub-05_ses-009_task-mario3_run-02_events.tsv} (100%) rename sub-05/ses-009/func/{sub-05_ses-009_task-mario3_run-02_part-mag_events.tsv => sub-05_ses-009_task-mario3_run-03_events.tsv} (100%) rename sub-05/ses-009/func/{sub-05_ses-009_task-mario3_run-02_part-phase_events.tsv => sub-05_ses-009_task-mario3_run-04_events.tsv} (100%) delete mode 120000 sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-04_part-mag_events.tsv delete mode 120000 sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-04_part-phase_events.tsv rename sub-05/ses-009/func/{sub-05_ses-009_task-mario3_run-03_part-mag_events.tsv => sub-05_ses-009_task-mario3_run-05_events.tsv} (100%) delete mode 120000 sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-05_part-mag_events.tsv delete mode 120000 sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-05_part-phase_events.tsv rename sub-05/ses-009/func/{sub-05_ses-009_task-mario3_run-03_part-phase_events.tsv => sub-05_ses-009_task-mario3_run-06_events.tsv} (100%) delete mode 120000 sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-mag_events.tsv delete mode 120000 sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-phase_events.tsv diff --git a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-01_part-mag_events.tsv b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-01_events.tsv similarity index 100% rename from sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-01_part-mag_events.tsv rename to sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-01_events.tsv diff --git a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-01_part-phase_events.tsv b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-02_events.tsv similarity index 100% rename from sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-01_part-phase_events.tsv rename to sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-02_events.tsv diff --git a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-02_part-mag_events.tsv b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-03_events.tsv similarity index 100% rename from sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-02_part-mag_events.tsv rename to sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-03_events.tsv diff --git a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-02_part-phase_events.tsv b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-04_events.tsv similarity index 100% rename from sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-02_part-phase_events.tsv rename to sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-04_events.tsv diff --git a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-04_part-mag_events.tsv b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-04_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-04_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-04_part-phase_events.tsv b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-04_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-04_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-03_part-mag_events.tsv b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-05_events.tsv similarity index 100% rename from sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-03_part-mag_events.tsv rename to sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-05_events.tsv diff --git a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-05_part-mag_events.tsv b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-05_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-05_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-05_part-phase_events.tsv b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-05_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-05_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-03_part-phase_events.tsv b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_events.tsv similarity index 100% rename from sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-03_part-phase_events.tsv rename to sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_events.tsv diff --git a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-mag_events.tsv b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-phase_events.tsv b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-06_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 38b6745bed604fb87ebc92a76db2f6a2d087ac5d Mon Sep 17 00:00:00 2001 From: test Date: Tue, 29 Aug 2023 15:32:38 -0400 Subject: [PATCH 445/463] fill IntendedFor --- ...5_ses-009_acq-sbref_dir-AP_run-01_epi.json | 90 ++----------------- ...5_ses-009_acq-sbref_dir-PA_run-04_epi.json | 88 ++---------------- ...5_ses-009_acq-sbref_dir-PA_run-05_epi.json | 88 ++---------------- ...5_ses-009_acq-sbref_dir-PA_run-06_epi.json | 88 ++---------------- 4 files changed, 30 insertions(+), 324 deletions(-) diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi.json index a90061588..7ef35dd4b 100644 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999892, - -0.0123771, - 0.00797348, - 0.0144857, - 0.923873, - -0.382425 - ], + "ImageOrientationPatientDICOM": [0.999892, -0.0123771, 0.00797348, 0.0144857, 0.923873, -0.382425], "ImageOrientationText": "Tra>Cor(-22.5)>Sag(0.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-009/func/sub-05_ses-009_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-009/func/sub-05_ses-009_task-mario3_run-05_part-mag_bold.nii.gz", + "ses-009/func/sub-05_ses-009_task-mario3_run-06_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-2_SBRef", "SeriesNumber": 23, - "ShimSetting": [ - 587, - -7295, - -8817, - 401, - 21, - -370, - -75, - 95 - ], + "ShimSetting": [587, -7295, -8817, 401, 21, -370, -75, 95], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.04, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.53, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.02, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.51, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.04, 3.1375, 3.235, 3.3325, 3.43, 3.53, 3.6275, 3.725, 3.8225, 3.92, 4.02, 4.1175, 4.215, 4.3125, 4.41, 4.51, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_epi.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_epi.json index 9e67d4a23..747a539da 100644 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999892, - -0.0123771, - 0.00797348, - 0.0144857, - 0.923873, - -0.382425 - ], + "ImageOrientationPatientDICOM": [0.999892, -0.0123771, 0.00797348, 0.0144857, 0.923873, -0.382425], "ImageOrientationText": "Tra>Cor(-22.5)>Sag(0.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-009/func/sub-05_ses-009_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 26, - "ShimSetting": [ - 588, - -7296, - -8818, - 399, - 23, - -371, - -74, - 95 - ], + "ShimSetting": [588, -7296, -8818, 399, 23, -371, -74, 95], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_epi.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_epi.json index c29e4d079..e88d1bc25 100644 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999892, - -0.0123771, - 0.00797348, - 0.0144857, - 0.923873, - -0.382425 - ], + "ImageOrientationPatientDICOM": [0.999892, -0.0123771, 0.00797348, 0.0144857, 0.923873, -0.382425], "ImageOrientationText": "Tra>Cor(-22.5)>Sag(0.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-009/func/sub-05_ses-009_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 29, - "ShimSetting": [ - 588, - -7296, - -8818, - 399, - 23, - -371, - -74, - 95 - ], + "ShimSetting": [588, -7296, -8818, 399, 23, -371, -74, 95], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_epi.json b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_epi.json index 89965e510..0c8a5ffc4 100644 --- a/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_epi.json +++ b/sub-05/ses-009/fmap/sub-05_ses-009_acq-sbref_dir-PA_run-06_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999892, - -0.0123771, - 0.00797348, - 0.0144857, - 0.923873, - -0.382425 - ], + "ImageOrientationPatientDICOM": [0.999892, -0.0123771, 0.00797348, 0.0144857, 0.923873, -0.382425], "ImageOrientationText": "Tra>Cor(-22.5)>Sag(0.2)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-009/func/sub-05_ses-009_task-mario3_run-06_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-06_SBRef", "SeriesNumber": 32, - "ShimSetting": [ - 588, - -7296, - -8818, - 399, - 23, - -371, - -74, - 95 - ], + "ShimSetting": [588, -7296, -8818, 399, 23, -371, -74, 95], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From c3c845e5701e6f2a128a19b8a000225dbe20c77f Mon Sep 17 00:00:00 2001 From: test Date: Tue, 29 Aug 2023 15:38:51 -0400 Subject: [PATCH 446/463] [DATALAD] Recorded changes --- .gitmodules | 4 ++++ .heudiconv | 1 + 2 files changed, 5 insertions(+) create mode 100644 .gitmodules create mode 160000 .heudiconv diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..331bff2ef --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule ".heudiconv"] + path = .heudiconv + url = ./.heudiconv + datalad-id = 6e2823e1-135d-44ce-ae0b-1ff0c0ab53ab diff --git a/.heudiconv b/.heudiconv new file mode 160000 index 000000000..3acd3f3a0 --- /dev/null +++ b/.heudiconv @@ -0,0 +1 @@ +Subproject commit 3acd3f3a0edcd724a842fd0d3fcab20bf57694dc From ef5ffdce0db8cb8bb02b2f428c90e5dbd0278d64 Mon Sep 17 00:00:00 2001 From: test Date: Tue, 29 Aug 2023 15:39:30 -0400 Subject: [PATCH 447/463] [DATALAD] Recorded changes --- .heudiconv | 2 +- CHANGES | 5 + participants.json | 14 + participants.tsv | 2 + scans.json | 16 + .../sub-05_ses-010_acq-axial_localizer.json | 81 +++ .../sub-05_ses-010_acq-axial_localizer.nii.gz | 1 + ...5_ses-010_acq-axial_localizer__dup-01.json | 81 +++ ...ses-010_acq-axial_localizer__dup-01.nii.gz | 1 + .../sub-05_ses-010_acq-coronal_localizer.json | 81 +++ ...ub-05_ses-010_acq-coronal_localizer.nii.gz | 1 + ...ses-010_acq-coronal_localizer__dup-01.json | 81 +++ ...s-010_acq-coronal_localizer__dup-01.nii.gz | 1 + ...sub-05_ses-010_acq-sagittal_localizer.json | 86 +++ ...b-05_ses-010_acq-sagittal_localizer.nii.gz | 1 + ...es-010_acq-sagittal_localizer__dup-01.json | 86 +++ ...-010_acq-sagittal_localizer__dup-01.nii.gz | 1 + sub-05/ses-010/anat/sub-05_ses-010_scout.json | 542 ++++++++++++++++++ .../ses-010/anat/sub-05_ses-010_scout.nii.gz | 1 + .../anat/sub-05_ses-010_scout__dup-01.json | 542 ++++++++++++++++++ .../anat/sub-05_ses-010_scout__dup-01.nii.gz | 1 + ...0_acq-bold_dir-AP_run-01_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ...0_acq-bold_dir-AP_run-02_part-mag_epi.json | 171 ++++++ ...acq-bold_dir-AP_run-02_part-mag_epi.nii.gz | 1 + ...acq-bold_dir-AP_run-02_part-phase_epi.json | 177 ++++++ ...q-bold_dir-AP_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-AP_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-AP_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-AP_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-AP_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-01_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-01_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-02_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-02_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-03_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-03_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-04_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-04_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-05_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-05_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-06_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-06_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-07_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-07_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-07_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-07_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-08_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-08_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-08_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-08_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-09_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-09_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-09_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-09_part-phase_epi.nii.gz | 1 + ..._acq-sbref_dir-PA_run-10_part-mag_epi.json | 149 +++++ ...cq-sbref_dir-PA_run-10_part-mag_epi.nii.gz | 1 + ...cq-sbref_dir-PA_run-10_part-phase_epi.json | 152 +++++ ...-sbref_dir-PA_run-10_part-phase_epi.nii.gz | 1 + ...-010_task-mario3_run-01_part-mag_bold.json | 172 ++++++ ...10_task-mario3_run-01_part-mag_bold.nii.gz | 1 + ...010_task-mario3_run-01_part-mag_events.tsv | 1 + ...010_task-mario3_run-01_part-mag_sbref.json | 150 +++++ ...0_task-mario3_run-01_part-mag_sbref.nii.gz | 1 + ...10_task-mario3_run-01_part-phase_bold.json | 178 ++++++ ..._task-mario3_run-01_part-phase_bold.nii.gz | 1 + ...0_task-mario3_run-01_part-phase_events.tsv | 1 + ...0_task-mario3_run-01_part-phase_sbref.json | 153 +++++ 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file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification) \ No newline at end of file diff --git a/participants.json b/participants.json new file mode 100644 index 000000000..0d9e3ad57 --- /dev/null +++ b/participants.json @@ -0,0 +1,14 @@ +{ + "participant_id": { + "Description": "Participant identifier" + }, + "age": { + "Description": "Age in years (TODO - verify) as in the initial session, might not be correct for other sessions" + }, + "sex": { + "Description": "self-rated by participant, M for male/F for female (TODO: verify)" + }, + "group": { + "Description": "(TODO: adjust - by default everyone is in control group)" + } +} \ No newline at end of file diff --git a/participants.tsv b/participants.tsv new file mode 100644 index 000000000..da8d4ae9f --- /dev/null +++ b/participants.tsv @@ -0,0 +1,2 @@ +participant_id age sex group +sub-05 50 M control diff --git a/scans.json b/scans.json new file mode 100644 index 000000000..8733b9e8c --- /dev/null +++ b/scans.json @@ -0,0 +1,16 @@ +{ + "filename": { + "Description": "Name of the nifti file" + }, + "acq_time": { + "LongName": "Acquisition time", + "Description": "Acquisition time of the particular scan" + }, + "operator": { + "Description": "Name of the operator" + }, + "randstr": { + "LongName": "Random string", + "Description": "md5 hash of UIDs" + } +} \ No newline at end of file diff --git a/sub-05/ses-010/anat/sub-05_ses-010_acq-axial_localizer.json b/sub-05/ses-010/anat/sub-05_ses-010_acq-axial_localizer.json new file mode 100644 index 000000000..fc5e4018a --- /dev/null +++ b/sub-05/ses-010/anat/sub-05_ses-010_acq-axial_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "19:34:30.000000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": 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+../../../.git/annex/objects/1x/Jq/MD5E-s178847--740a1ee01820e93973ba08d8ec3575cb.nii.gz/MD5E-s178847--740a1ee01820e93973ba08d8ec3575cb.nii.gz \ No newline at end of file diff --git a/sub-05/ses-010/anat/sub-05_ses-010_acq-axial_localizer__dup-01.json b/sub-05/ses-010/anat/sub-05_ses-010_acq-axial_localizer__dup-01.json new file mode 100644 index 000000000..2eea9b079 --- /dev/null +++ b/sub-05/ses-010/anat/sub-05_ses-010_acq-axial_localizer__dup-01.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:07:22.027500", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 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a/sub-05/ses-010/anat/sub-05_ses-010_acq-coronal_localizer.json b/sub-05/ses-010/anat/sub-05_ses-010_acq-coronal_localizer.json new file mode 100644 index 000000000..21168988c --- /dev/null +++ b/sub-05/ses-010/anat/sub-05_ses-010_acq-coronal_localizer.json @@ -0,0 +1,81 @@ +{ + "AcquisitionMatrixPE": 233, + "AcquisitionNumber": 1, + "AcquisitionTime": "19:34:36.990000", + "BaseResolution": 256, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Adaptive Combine", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DeviceSerialNumber": "167006", + "DwellTime": 6.1e-06, + "EchoTime": 0.00369, + "FlipAngle": 20, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageOrientationPatientDICOM": [ + 1, + 0, + 0, + 0, + 0, + -1 + ], + "ImageOrientationText": "Cor", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "NORM", + "DIS2D" + ], + "ImagingFrequency": 123.259, + 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new file mode 100644 index 000000000..fb7266843 --- /dev/null +++ b/sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-02_part-phase_epi.json @@ -0,0 +1,177 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "19:35:30.812500", + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTime1": 0.037, + "EchoTime2": 0.001, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImageOrientationPatientDICOM": [0.999832, -0.0126643, 0.0132834, 0.0169285, 0.915955, -0.400923], + 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"WindowCenter": [4856.0, 4880.0, 4868.0], + "WindowWidth": [18632.0, 18666.0, 18672.0] + }, + "slices": {} + } +} \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-02_part-phase_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-02_part-phase_epi.nii.gz new file mode 120000 index 000000000..4f81795ec --- /dev/null +++ b/sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-02_part-phase_epi.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/mf/xZ/MD5E-s3334179--8ef2e46a306e773dd3129a7b9dff189f.nii.gz/MD5E-s3334179--8ef2e46a306e773dd3129a7b9dff189f.nii.gz \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.json new file mode 100644 index 000000000..3d8ecbc78 --- /dev/null +++ b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.json @@ -0,0 +1,149 @@ +{ + 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+} \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz new file mode 120000 index 000000000..cc227d995 --- /dev/null +++ b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/8w/fW/MD5E-s1116760--1075fadb74a4c1504f54b4fad05a7166.nii.gz/MD5E-s1116760--1075fadb74a4c1504f54b4fad05a7166.nii.gz \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json new file mode 100644 index 000000000..7ae160091 --- /dev/null +++ b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json @@ -0,0 +1,152 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "AcquisitionTime": "18:08:16.952500", + 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a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-10_part-phase_sbref.nii.gz b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-10_part-phase_sbref.nii.gz new file mode 120000 index 000000000..74dea0c56 --- /dev/null +++ b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-10_part-phase_sbref.nii.gz @@ -0,0 +1 @@ +../../../.git/annex/objects/1g/vG/MD5E-s1103614--78523b3e18d754687a8dbde879cc2cdc.nii.gz/MD5E-s1103614--78523b3e18d754687a8dbde879cc2cdc.nii.gz \ No newline at end of file diff --git a/sub-05/ses-010/sub-05_ses-010_scans.tsv b/sub-05/ses-010/sub-05_ses-010_scans.tsv new file mode 120000 index 000000000..3139d8b74 --- /dev/null +++ b/sub-05/ses-010/sub-05_ses-010_scans.tsv @@ -0,0 +1 @@ +../../.git/annex/objects/mf/jQ/MD5E-s7818--b79fae0bcfbdd6c5f18182877e8d9c38.tsv/MD5E-s7818--b79fae0bcfbdd6c5f18182877e8d9c38.tsv \ No newline at end of file diff --git a/task-mario3_bold.json b/task-mario3_bold.json new file mode 100644 index 000000000..c2df6e4b1 --- /dev/null +++ b/task-mario3_bold.json @@ -0,0 +1,64 @@ +{ + "AcquisitionMatrixPE": 104, + "AcquisitionNumber": 1, + "BandwidthPerPixelPhaseEncode": 17.17, + "BaseResolution": 104, + "BodyPartExamined": "BRAIN", + "CogAtlasID": "http://www.cognitiveatlas.org/task/id/TODO", + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11C_LATEST_20160120", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20220505", + "DerivedVendorReportedEchoSpacing": 0.000560011, + "DeviceSerialNumber": "167006", + "DwellTime": 2.1e-06, + "EchoTime": 0.037, + "EchoTrainLength": 104, + "EffectiveEchoSpacing": 0.000560011, + "FlipAngle": 52, + "HeudiconvVersion": "0.5.3.post811+g6206e14", + "ImageComments": "Unaliased MB4/PE3/LB", + "ImagingFrequency": 123.259, + "InPlanePhaseEncodingDirectionDICOM": "COL", + "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", + "InstitutionName": "IUGM", + "InstitutionalDepartmentName": "Department", + "MRAcquisitionType": "2D", + "MagneticFieldStrength": 3, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "MatrixCoilMode": "SENSE", + "Modality": "MR", + "MultibandAccelerationFactor": 4, + "PartialFourier": 1, + "PatientPosition": "HFS", + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "PhaseEncodingDirection": "j", + "PhaseEncodingSteps": 104, + "PhaseResolution": 1, + "PixelBandwidth": 2290, + "ProcedureStepDescription": "games^mario3", + "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", + "ReceiveCoilActiveElements": "HC1-7;NC1,2", + "ReceiveCoilName": "HeadNeck_64", + "ReconMatrixPE": 104, + "RepetitionTime": 1.49, + "ScanOptions": "FS", + "ScanningSequence": "EP", + "SequenceName": "epfid2d1_104", + "SequenceVariant": "SK\\SS", + "SliceThickness": 2, + "SoftwareVersions": "syngo MR E11", + "SpacingBetweenSlices": 2, + "StationName": "MRC35049", + "TaskName": "TODO: full task name for mario3", + "TotalReadoutTime": 0.0576811, + "dcmmeta_reorient_transform": [ + [0.0, -1.0, 0.0, 103.0], + [1.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0] +], + "dcmmeta_slice_dim": 2, + "dcmmeta_version": 0.6} \ No newline at end of file From 881849828f8ca1b403a9101e086fb4cb7fca88b9 Mon Sep 17 00:00:00 2001 From: test Date: Tue, 29 Aug 2023 15:40:11 -0400 Subject: [PATCH 448/463] fix fmap phase --- ...5_ses-010_acq-bold_dir-AP_run-01_epi.json} | 0 ...ses-010_acq-bold_dir-AP_run-01_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-01_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ...5_ses-010_acq-bold_dir-AP_run-02_epi.json} | 0 ...ses-010_acq-bold_dir-AP_run-02_epi.nii.gz} | 0 ...acq-bold_dir-AP_run-02_part-phase_epi.json | 177 ------------------ ...q-bold_dir-AP_run-02_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-AP_run-01_epi.json} | 0 ...es-010_acq-sbref_dir-AP_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-01_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-AP_run-02_epi.json} | 0 ...es-010_acq-sbref_dir-AP_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-AP_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-AP_run-02_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-PA_run-01_epi.json} | 0 ...es-010_acq-sbref_dir-PA_run-01_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-01_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-01_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-PA_run-02_epi.json} | 0 ...es-010_acq-sbref_dir-PA_run-02_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-02_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-02_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-PA_run-03_epi.json} | 0 ...es-010_acq-sbref_dir-PA_run-03_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-03_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-03_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-PA_run-04_epi.json} | 0 ...es-010_acq-sbref_dir-PA_run-04_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-04_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-04_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-PA_run-05_epi.json} | 0 ...es-010_acq-sbref_dir-PA_run-05_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-05_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-05_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-PA_run-06_epi.json} | 0 ...es-010_acq-sbref_dir-PA_run-06_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-06_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-06_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-PA_run-07_epi.json} | 0 ...es-010_acq-sbref_dir-PA_run-07_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-07_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-07_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-PA_run-08_epi.json} | 0 ...es-010_acq-sbref_dir-PA_run-08_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-08_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-08_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-PA_run-09_epi.json} | 0 ...es-010_acq-sbref_dir-PA_run-09_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-09_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-09_part-phase_epi.nii.gz | 1 - ..._ses-010_acq-sbref_dir-PA_run-10_epi.json} | 0 ...es-010_acq-sbref_dir-PA_run-10_epi.nii.gz} | 0 ...cq-sbref_dir-PA_run-10_part-phase_epi.json | 152 --------------- ...-sbref_dir-PA_run-10_part-phase_epi.nii.gz | 1 - sub-05/ses-010/sub-05_ses-010_scans.tsv | 2 +- 57 files changed, 1 insertion(+), 2193 deletions(-) rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.json => sub-05_ses-010_acq-bold_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-010_acq-bold_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-bold_dir-AP_run-02_part-mag_epi.json => sub-05_ses-010_acq-bold_dir-AP_run-02_epi.json} (100%) rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-bold_dir-AP_run-02_part-mag_epi.nii.gz => sub-05_ses-010_acq-bold_dir-AP_run-02_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-02_part-phase_epi.json delete mode 120000 sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-02_part-phase_epi.nii.gz rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.json => sub-05_ses-010_acq-sbref_dir-AP_run-01_epi.json} (100%) rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz => sub-05_ses-010_acq-sbref_dir-AP_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-AP_run-02_part-mag_epi.json => sub-05_ses-010_acq-sbref_dir-AP_run-02_epi.json} (100%) rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-AP_run-02_part-mag_epi.nii.gz => sub-05_ses-010_acq-sbref_dir-AP_run-02_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-02_part-phase_epi.json delete mode 120000 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-02_part-phase_epi.nii.gz rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.json => sub-05_ses-010_acq-sbref_dir-PA_run-01_epi.json} (100%) rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz => sub-05_ses-010_acq-sbref_dir-PA_run-01_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json delete mode 120000 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.json => sub-05_ses-010_acq-sbref_dir-PA_run-02_epi.json} (100%) rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz => sub-05_ses-010_acq-sbref_dir-PA_run-02_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json delete mode 120000 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.json => sub-05_ses-010_acq-sbref_dir-PA_run-03_epi.json} (100%) rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz => sub-05_ses-010_acq-sbref_dir-PA_run-03_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.json delete mode 120000 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-04_part-mag_epi.json => sub-05_ses-010_acq-sbref_dir-PA_run-04_epi.json} (100%) rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz => sub-05_ses-010_acq-sbref_dir-PA_run-04_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_part-phase_epi.json delete mode 120000 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-05_part-mag_epi.json => sub-05_ses-010_acq-sbref_dir-PA_run-05_epi.json} (100%) rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz => sub-05_ses-010_acq-sbref_dir-PA_run-05_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_part-phase_epi.json delete mode 120000 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-06_part-mag_epi.json => sub-05_ses-010_acq-sbref_dir-PA_run-06_epi.json} (100%) rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz => sub-05_ses-010_acq-sbref_dir-PA_run-06_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-06_part-phase_epi.json delete mode 120000 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-06_part-phase_epi.nii.gz rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-07_part-mag_epi.json => sub-05_ses-010_acq-sbref_dir-PA_run-07_epi.json} (100%) rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz => sub-05_ses-010_acq-sbref_dir-PA_run-07_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-07_part-phase_epi.json delete mode 120000 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-08_part-mag_epi.json => sub-05_ses-010_acq-sbref_dir-PA_run-08_epi.json} (100%) rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-08_part-mag_epi.nii.gz => sub-05_ses-010_acq-sbref_dir-PA_run-08_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-08_part-phase_epi.json delete mode 120000 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-08_part-phase_epi.nii.gz rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-09_part-mag_epi.json => sub-05_ses-010_acq-sbref_dir-PA_run-09_epi.json} (100%) rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-09_part-mag_epi.nii.gz => sub-05_ses-010_acq-sbref_dir-PA_run-09_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_part-phase_epi.json delete mode 120000 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_part-phase_epi.nii.gz rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-10_part-mag_epi.json => sub-05_ses-010_acq-sbref_dir-PA_run-10_epi.json} (100%) rename sub-05/ses-010/fmap/{sub-05_ses-010_acq-sbref_dir-PA_run-10_part-mag_epi.nii.gz => sub-05_ses-010_acq-sbref_dir-PA_run-10_epi.nii.gz} (100%) delete mode 100644 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_part-phase_epi.json delete mode 120000 sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_part-phase_epi.nii.gz diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-01_epi.json similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.json rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-01_epi.json diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 19a1acae6..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:08:27.382500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.99942, -0.0307991, 0.0145336, 0.0340273, 0.920597, -0.389028], - "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "MB", - "ND", - "MOSAIC", - "PHASE" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - 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-../../../.git/annex/objects/5z/jQ/MD5E-s3334158--53704070a6bee47e561dca544b69e059.nii.gz/MD5E-s3334158--53704070a6bee47e561dca544b69e059.nii.gz \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-02_part-mag_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-02_epi.json similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-02_part-mag_epi.json rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-02_epi.json diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-02_part-mag_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-02_epi.nii.gz similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-02_part-mag_epi.nii.gz rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-02_epi.nii.gz diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-02_part-phase_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-02_part-phase_epi.json deleted file mode 100644 index fb7266843..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-bold_dir-AP_run-02_part-phase_epi.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:35:30.812500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - 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rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_epi.json diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_part-mag_epi.nii.gz rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_epi.nii.gz diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json deleted file mode 100644 index 7ae160091..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:08:16.952500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": 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b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz deleted file mode 120000 index e4796e633..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/29/k1/MD5E-s1112217--3a67c32a568129ccf2b49cc0acd89a9e.nii.gz/MD5E-s1112217--3a67c32a568129ccf2b49cc0acd89a9e.nii.gz \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-02_part-mag_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-02_epi.json similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-02_part-mag_epi.json rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-02_epi.json diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-02_part-mag_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-02_epi.nii.gz similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-02_part-mag_epi.nii.gz rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-02_epi.nii.gz diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-02_part-phase_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-02_part-phase_epi.json deleted file mode 100644 index 03d2a647c..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:35:20.382500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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-../../../.git/annex/objects/Zx/JV/MD5E-s1112105--36477d0df0914d3a3af36c2d624b852f.nii.gz/MD5E-s1112105--36477d0df0914d3a3af36c2d624b852f.nii.gz \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_epi.json similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.json rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_epi.json diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_epi.nii.gz similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_part-mag_epi.nii.gz rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_epi.nii.gz diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json deleted file mode 100644 index b7bd821ad..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:09:54.727500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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"%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0573551, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-01_SBRef", - "SeriesNumber": 9, - "ShimSetting": [ - 585, - -7292, - -8813, - 375, - 24, - -372, - -69, - 94 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 266.736, - "WipMemBlock": "270c6190-7a4c-40a7-b72c-e99c91c43e75||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz deleted file mode 120000 index a9274aeda..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/6g/6k/MD5E-s1103383--f4d1397c461e3a5aeafb80eb8f47bb0a.nii.gz/MD5E-s1103383--f4d1397c461e3a5aeafb80eb8f47bb0a.nii.gz \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_epi.json similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.json rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_epi.json diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_epi.nii.gz similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_part-mag_epi.nii.gz rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_epi.nii.gz diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json deleted file mode 100644 index 578756f93..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:20:33.175000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99942, - -0.0307991, - 0.0145336, - 0.0340273, - 0.920597, - -0.389028 - ], - "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - 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"SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-02_SBRef", - "SeriesNumber": 12, - "ShimSetting": [ - 585, - -7292, - -8813, - 375, - 24, - -372, - -69, - 94 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 266.736, - "WipMemBlock": "64735877-7850-40fe-8800-4c6505602171||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz deleted file mode 120000 index b7f9ee8d2..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/x1/VJ/MD5E-s1103562--0d1f455242c4e8d3a53113a9f6d5316a.nii.gz/MD5E-s1103562--0d1f455242c4e8d3a53113a9f6d5316a.nii.gz \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_epi.json similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.json rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_epi.json diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_epi.nii.gz similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_part-mag_epi.nii.gz rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_epi.nii.gz diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.json deleted file mode 100644 index 60fbcf5da..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:30:13.592500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99942, - -0.0307991, - 0.0145336, - 0.0340273, - 0.920597, - -0.389028 - ], - "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-03", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0573551, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-03_SBRef", - "SeriesNumber": 15, - "ShimSetting": [ - 585, - -7292, - -8813, - 375, - 24, - -372, - -69, - 94 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 266.736, - "WipMemBlock": "2984ad65-9123-4d47-adc4-9230afcfe983||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz deleted file mode 120000 index 4ca853ef7..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Q9/FW/MD5E-s1103366--80679c8c637b97372d51e88dc5aa7960.nii.gz/MD5E-s1103366--80679c8c637b97372d51e88dc5aa7960.nii.gz \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_part-mag_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_epi.json similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_part-mag_epi.json rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_epi.json diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_epi.nii.gz similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_part-mag_epi.nii.gz rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_epi.nii.gz diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_part-phase_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_part-phase_epi.json deleted file mode 100644 index 6179e1601..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:40:53.072500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99942, - -0.0307991, - 0.0145336, - 0.0340273, - 0.920597, - -0.389028 - ], - "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-04", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0573551, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-04_SBRef", - "SeriesNumber": 18, - "ShimSetting": [ - 585, - -7292, - -8813, - 375, - 24, - -372, - -69, - 94 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 266.736, - "WipMemBlock": "4063a6f6-0350-4cc9-902d-88a6ae128222||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz deleted file mode 120000 index 8fe8a2eb0..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/06/pk/MD5E-s1103557--ede65b63ca1bd94056e38742450e8834.nii.gz/MD5E-s1103557--ede65b63ca1bd94056e38742450e8834.nii.gz \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_part-mag_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_epi.json similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_part-mag_epi.json rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_epi.json diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_epi.nii.gz similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_part-mag_epi.nii.gz rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_epi.nii.gz diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_part-phase_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_part-phase_epi.json deleted file mode 100644 index c1621da29..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:50:44.837500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99942, - -0.0307991, - 0.0145336, - 0.0340273, - 0.920597, - -0.389028 - ], - "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-05", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0573551, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-05_SBRef", - "SeriesNumber": 21, - "ShimSetting": [ - 585, - -7292, - -8813, - 375, - 24, - -372, - -69, - 94 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 266.736, - "WipMemBlock": "44623be2-9c73-4216-9bb9-2209674a2d65||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz deleted file mode 120000 index d170ffd79..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/2m/Q6/MD5E-s1103470--7bc415c477a33cde05bbe2fd044745b9.nii.gz/MD5E-s1103470--7bc415c477a33cde05bbe2fd044745b9.nii.gz \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-06_part-mag_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-06_epi.json similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-06_part-mag_epi.json rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-06_epi.json diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-06_epi.nii.gz similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-06_part-mag_epi.nii.gz rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-06_epi.nii.gz diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-06_part-phase_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-06_part-phase_epi.json deleted file mode 100644 index 643e3b582..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-06_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:02:13.110000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99942, - -0.0307991, - 0.0145336, - 0.0340273, - 0.920597, - -0.389028 - ], - "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-06", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0573551, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - 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sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-07_epi.json diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-07_epi.nii.gz similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-07_part-mag_epi.nii.gz rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-07_epi.nii.gz diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-07_part-phase_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-07_part-phase_epi.json deleted file mode 100644 index 1e753e8c5..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-07_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:12:17.772500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of 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b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz deleted file mode 120000 index 63f8f4e4b..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-07_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/8m/7p/MD5E-s1103434--9966efa1a9c23850f99b0c250e450cbe.nii.gz/MD5E-s1103434--9966efa1a9c23850f99b0c250e450cbe.nii.gz \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-08_part-mag_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-08_epi.json similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-08_part-mag_epi.json rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-08_epi.json diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-08_part-mag_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-08_epi.nii.gz similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-08_part-mag_epi.nii.gz rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-08_epi.nii.gz diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-08_part-phase_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-08_part-phase_epi.json deleted file mode 100644 index b65c61f7e..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-08_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:36:30.532500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 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"PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-08", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0635022, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-08_SBRef", - "SeriesNumber": 38, - "ShimSetting": [ - 593, - -7311, - -8817, - 363, - 39, - -414, - -59, - 92 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, 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-../../../.git/annex/objects/zM/4J/MD5E-s1103565--beab132d1dbea4f05c50aa82ef5332fb.nii.gz/MD5E-s1103565--beab132d1dbea4f05c50aa82ef5332fb.nii.gz \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_part-mag_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_epi.json similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_part-mag_epi.json rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_epi.json diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_part-mag_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_epi.nii.gz similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_part-mag_epi.nii.gz rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_epi.nii.gz diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_part-phase_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_part-phase_epi.json deleted file mode 100644 index 762298958..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:47:23.880000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - 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"%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0635022, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-09_SBRef", - "SeriesNumber": 41, - "ShimSetting": [ - 593, - -7311, - -8817, - 363, - 39, - -414, - -59, - 92 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 272.473, - "WipMemBlock": "4ee8e02b-0d61-4a57-be41-e54f2de392eb||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_part-phase_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_part-phase_epi.nii.gz deleted file mode 120000 index f8f5bf320..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/29/1p/MD5E-s1103477--91aedd3eb6e3fa1631c07fa6e84a50a5.nii.gz/MD5E-s1103477--91aedd3eb6e3fa1631c07fa6e84a50a5.nii.gz \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_part-mag_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_epi.json similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_part-mag_epi.json rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_epi.json diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_part-mag_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_epi.nii.gz similarity index 100% rename from sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_part-mag_epi.nii.gz rename to sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_epi.nii.gz diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_part-phase_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_part-phase_epi.json deleted file mode 100644 index 11733f283..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_part-phase_epi.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "19:57:42.127500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTime1": 0.037, - "EchoTime2": 0.001, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999832, - -0.0126643, - 0.0132834, - 0.0169285, - 0.915955, - -0.400923 - ], - "ImageOrientationText": "Tra>Cor(-23.6)>Sag(0.4)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "P", - "ND", - "MOSAIC", - "PHASE" - ], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_task-mario3_run-10", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0635022, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_task-mario3_run-10_SBRef", - "SeriesNumber": 44, - "ShimSetting": [ - 593, - -7311, - -8817, - 363, - 39, - -414, - -59, - 92 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 272.473, - "WipMemBlock": "7839ef88-0390-43ca-b40f-229761d4ed0a||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_part-phase_epi.nii.gz b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_part-phase_epi.nii.gz deleted file mode 120000 index 74dea0c56..000000000 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_part-phase_epi.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/1g/vG/MD5E-s1103614--78523b3e18d754687a8dbde879cc2cdc.nii.gz/MD5E-s1103614--78523b3e18d754687a8dbde879cc2cdc.nii.gz \ No newline at end of file diff --git a/sub-05/ses-010/sub-05_ses-010_scans.tsv b/sub-05/ses-010/sub-05_ses-010_scans.tsv index 3139d8b74..66ce659de 120000 --- a/sub-05/ses-010/sub-05_ses-010_scans.tsv +++ b/sub-05/ses-010/sub-05_ses-010_scans.tsv @@ -1 +1 @@ -../../.git/annex/objects/mf/jQ/MD5E-s7818--b79fae0bcfbdd6c5f18182877e8d9c38.tsv/MD5E-s7818--b79fae0bcfbdd6c5f18182877e8d9c38.tsv \ No newline at end of file +../../.git/annex/objects/5m/45/MD5E-s6133--5e295728811506777b6863b9913a4300.tsv/MD5E-s6133--5e295728811506777b6863b9913a4300.tsv \ No newline at end of file From 007961a3ac50bd2df4f3408114067380e7579be5 Mon Sep 17 00:00:00 2001 From: test Date: Tue, 29 Aug 2023 15:40:22 -0400 Subject: [PATCH 449/463] fix complex event files --- ...g_events.tsv => sub-05_ses-010_task-mario3_run-01_events.tsv} | 0 ...e_events.tsv => sub-05_ses-010_task-mario3_run-02_events.tsv} | 0 ...g_events.tsv => sub-05_ses-010_task-mario3_run-03_events.tsv} | 0 ...e_events.tsv => sub-05_ses-010_task-mario3_run-04_events.tsv} | 0 ...g_events.tsv => sub-05_ses-010_task-mario3_run-05_events.tsv} | 0 ...e_events.tsv => sub-05_ses-010_task-mario3_run-06_events.tsv} | 0 .../func/sub-05_ses-010_task-mario3_run-06_part-mag_events.tsv | 1 - .../func/sub-05_ses-010_task-mario3_run-06_part-phase_events.tsv | 1 - ...g_events.tsv => sub-05_ses-010_task-mario3_run-07_events.tsv} | 0 .../func/sub-05_ses-010_task-mario3_run-07_part-mag_events.tsv | 1 - .../func/sub-05_ses-010_task-mario3_run-07_part-phase_events.tsv | 1 - ...e_events.tsv => sub-05_ses-010_task-mario3_run-08_events.tsv} | 0 .../func/sub-05_ses-010_task-mario3_run-08_part-mag_events.tsv | 1 - .../func/sub-05_ses-010_task-mario3_run-08_part-phase_events.tsv | 1 - ...g_events.tsv => sub-05_ses-010_task-mario3_run-09_events.tsv} | 0 .../func/sub-05_ses-010_task-mario3_run-09_part-mag_events.tsv | 1 - .../func/sub-05_ses-010_task-mario3_run-09_part-phase_events.tsv | 1 - ...e_events.tsv => sub-05_ses-010_task-mario3_run-10_events.tsv} | 0 .../func/sub-05_ses-010_task-mario3_run-10_part-mag_events.tsv | 1 - .../func/sub-05_ses-010_task-mario3_run-10_part-phase_events.tsv | 1 - 20 files changed, 10 deletions(-) rename sub-05/ses-010/func/{sub-05_ses-010_task-mario3_run-01_part-mag_events.tsv => sub-05_ses-010_task-mario3_run-01_events.tsv} (100%) rename sub-05/ses-010/func/{sub-05_ses-010_task-mario3_run-01_part-phase_events.tsv => sub-05_ses-010_task-mario3_run-02_events.tsv} (100%) rename sub-05/ses-010/func/{sub-05_ses-010_task-mario3_run-02_part-mag_events.tsv => sub-05_ses-010_task-mario3_run-03_events.tsv} (100%) rename sub-05/ses-010/func/{sub-05_ses-010_task-mario3_run-02_part-phase_events.tsv => sub-05_ses-010_task-mario3_run-04_events.tsv} (100%) rename sub-05/ses-010/func/{sub-05_ses-010_task-mario3_run-03_part-mag_events.tsv => sub-05_ses-010_task-mario3_run-05_events.tsv} (100%) rename sub-05/ses-010/func/{sub-05_ses-010_task-mario3_run-03_part-phase_events.tsv => sub-05_ses-010_task-mario3_run-06_events.tsv} (100%) delete mode 120000 sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-06_part-mag_events.tsv delete mode 120000 sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-06_part-phase_events.tsv rename sub-05/ses-010/func/{sub-05_ses-010_task-mario3_run-04_part-mag_events.tsv => sub-05_ses-010_task-mario3_run-07_events.tsv} (100%) delete mode 120000 sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-07_part-mag_events.tsv delete mode 120000 sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-07_part-phase_events.tsv rename sub-05/ses-010/func/{sub-05_ses-010_task-mario3_run-04_part-phase_events.tsv => sub-05_ses-010_task-mario3_run-08_events.tsv} (100%) delete mode 120000 sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-08_part-mag_events.tsv delete mode 120000 sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-08_part-phase_events.tsv rename sub-05/ses-010/func/{sub-05_ses-010_task-mario3_run-05_part-mag_events.tsv => sub-05_ses-010_task-mario3_run-09_events.tsv} (100%) delete mode 120000 sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-09_part-mag_events.tsv delete mode 120000 sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-09_part-phase_events.tsv rename sub-05/ses-010/func/{sub-05_ses-010_task-mario3_run-05_part-phase_events.tsv => sub-05_ses-010_task-mario3_run-10_events.tsv} (100%) delete mode 120000 sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-10_part-mag_events.tsv delete mode 120000 sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-10_part-phase_events.tsv diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-01_part-mag_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-01_events.tsv similarity index 100% rename from sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-01_part-mag_events.tsv rename to sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-01_events.tsv diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-01_part-phase_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-02_events.tsv similarity index 100% rename from sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-01_part-phase_events.tsv rename to sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-02_events.tsv diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-02_part-mag_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-03_events.tsv similarity index 100% rename from sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-02_part-mag_events.tsv rename to sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-03_events.tsv diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-02_part-phase_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-04_events.tsv similarity index 100% rename from sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-02_part-phase_events.tsv rename to sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-04_events.tsv diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-03_part-mag_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-05_events.tsv similarity index 100% rename from sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-03_part-mag_events.tsv rename to sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-05_events.tsv diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-03_part-phase_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-06_events.tsv similarity index 100% rename from sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-03_part-phase_events.tsv rename to sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-06_events.tsv diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-06_part-mag_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-06_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-06_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-06_part-phase_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-06_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-06_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-04_part-mag_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-07_events.tsv similarity index 100% rename from sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-04_part-mag_events.tsv rename to sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-07_events.tsv diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-07_part-mag_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-07_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-07_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-07_part-phase_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-07_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-07_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-04_part-phase_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-08_events.tsv similarity index 100% rename from sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-04_part-phase_events.tsv rename to sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-08_events.tsv diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-08_part-mag_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-08_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-08_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-08_part-phase_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-08_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-08_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-05_part-mag_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-09_events.tsv similarity index 100% rename from sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-05_part-mag_events.tsv rename to sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-09_events.tsv diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-09_part-mag_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-09_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-09_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-09_part-phase_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-09_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-09_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-05_part-phase_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-10_events.tsv similarity index 100% rename from sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-05_part-phase_events.tsv rename to sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-10_events.tsv diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-10_part-mag_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-10_part-mag_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-10_part-mag_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-10_part-phase_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-10_part-phase_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-10_part-phase_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file From 0cf2223243d3f9456f453b37de38820b22c93a07 Mon Sep 17 00:00:00 2001 From: test Date: Tue, 29 Aug 2023 15:40:36 -0400 Subject: [PATCH 450/463] fill IntendedFor --- ...5_ses-010_acq-sbref_dir-AP_run-01_epi.json | 94 +++---------------- ...5_ses-010_acq-sbref_dir-AP_run-02_epi.json | 90 ++---------------- ...5_ses-010_acq-sbref_dir-PA_run-01_epi.json | 88 ++--------------- ...5_ses-010_acq-sbref_dir-PA_run-02_epi.json | 88 ++--------------- ...5_ses-010_acq-sbref_dir-PA_run-03_epi.json | 88 ++--------------- ...5_ses-010_acq-sbref_dir-PA_run-04_epi.json | 88 ++--------------- ...5_ses-010_acq-sbref_dir-PA_run-05_epi.json | 88 ++--------------- ...5_ses-010_acq-sbref_dir-PA_run-06_epi.json | 88 ++--------------- ...5_ses-010_acq-sbref_dir-PA_run-07_epi.json | 88 ++--------------- ...5_ses-010_acq-sbref_dir-PA_run-08_epi.json | 88 ++--------------- ...5_ses-010_acq-sbref_dir-PA_run-09_epi.json | 88 ++--------------- ...5_ses-010_acq-sbref_dir-PA_run-10_epi.json | 88 ++--------------- 12 files changed, 92 insertions(+), 972 deletions(-) diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_epi.json index 3d8ecbc78..ba199f86c 100644 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_epi.json +++ b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99942, - -0.0307991, - 0.0145336, - 0.0340273, - 0.920597, - -0.389028 - ], + "ImageOrientationPatientDICOM": [0.99942, -0.0307991, 0.0145336, 0.0340273, 0.920597, -0.389028], "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,21 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-05_ses-010_task-mario3_run-01_part-mag_bold.nii.gz", + "ses-010/func/sub-05_ses-010_task-mario3_run-02_part-mag_bold.nii.gz", + "ses-010/func/sub-05_ses-010_task-mario3_run-03_part-mag_bold.nii.gz", + "ses-010/func/sub-05_ses-010_task-mario3_run-04_part-mag_bold.nii.gz", + "ses-010/func/sub-05_ses-010_task-mario3_run-05_part-mag_bold.nii.gz", + "ses-010/func/sub-05_ses-010_task-mario3_run-06_part-mag_bold.nii.gz", + "ses-010/func/sub-05_ses-010_task-mario3_run-07_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +69,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-1_SBRef", "SeriesNumber": 6, - "ShimSetting": [ - 585, - -7292, - -8813, - 374, - 24, - -371, - -69, - 94 - ], + "ShimSetting": [585, -7292, -8813, 374, 24, -371, -69, 94], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.3325, 3.43, 3.5275, 3.625, 3.7225, 3.8225, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-02_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-02_epi.json index 8eeba8a14..e1add049e 100644 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-02_epi.json +++ b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-AP_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999832, - -0.0126643, - 0.0132834, - 0.0169285, - 0.915955, - -0.400923 - ], + "ImageOrientationPatientDICOM": [0.999832, -0.0126643, 0.0132834, 0.0169285, 0.915955, -0.400923], "ImageOrientationText": "Tra>Cor(-23.6)>Sag(0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,17 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-05_ses-010_task-mario3_run-08_part-mag_bold.nii.gz", + "ses-010/func/sub-05_ses-010_task-mario3_run-09_part-mag_bold.nii.gz", + "ses-010/func/sub-05_ses-010_task-mario3_run-10_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +65,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_AP_run-2_SBRef", "SeriesNumber": 35, - "ShimSetting": [ - 593, - -7311, - -8817, - 363, - 39, - -414, - -59, - 92 - ], + "ShimSetting": [593, -7311, -8817, 363, 39, -414, -59, 92], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.9775, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_epi.json index cc404978b..5aad02807 100644 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_epi.json +++ b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-01_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99942, - -0.0307991, - 0.0145336, - 0.0340273, - 0.920597, - -0.389028 - ], + "ImageOrientationPatientDICOM": [0.99942, -0.0307991, 0.0145336, 0.0340273, 0.920597, -0.389028], "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-05_ses-010_task-mario3_run-01_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-01_SBRef", "SeriesNumber": 9, - "ShimSetting": [ - 585, - -7292, - -8813, - 375, - 24, - -372, - -69, - 94 - ], + "ShimSetting": [585, -7292, -8813, 375, 24, -372, -69, 94], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.685, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.6825, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_epi.json index c68a0751d..1e43e1835 100644 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_epi.json +++ b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-02_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99942, - -0.0307991, - 0.0145336, - 0.0340273, - 0.920597, - -0.389028 - ], + "ImageOrientationPatientDICOM": [0.99942, -0.0307991, 0.0145336, 0.0340273, 0.920597, -0.389028], "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-05_ses-010_task-mario3_run-02_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-02_SBRef", "SeriesNumber": 12, - "ShimSetting": [ - 585, - -7292, - -8813, - 375, - 24, - -372, - -69, - 94 - ], + "ShimSetting": [585, -7292, -8813, 375, 24, -372, -69, 94], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_epi.json index 5c078a35d..378a8d816 100644 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_epi.json +++ b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-03_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99942, - -0.0307991, - 0.0145336, - 0.0340273, - 0.920597, - -0.389028 - ], + "ImageOrientationPatientDICOM": [0.99942, -0.0307991, 0.0145336, 0.0340273, 0.920597, -0.389028], "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-05_ses-010_task-mario3_run-03_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-03_SBRef", "SeriesNumber": 15, - "ShimSetting": [ - 585, - -7292, - -8813, - 375, - 24, - -372, - -69, - 94 - ], + "ShimSetting": [585, -7292, -8813, 375, 24, -372, -69, 94], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_epi.json index 893ded8f0..b14e7675d 100644 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_epi.json +++ b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-04_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99942, - -0.0307991, - 0.0145336, - 0.0340273, - 0.920597, - -0.389028 - ], + "ImageOrientationPatientDICOM": [0.99942, -0.0307991, 0.0145336, 0.0340273, 0.920597, -0.389028], "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-05_ses-010_task-mario3_run-04_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-04_SBRef", "SeriesNumber": 18, - "ShimSetting": [ - 585, - -7292, - -8813, - 375, - 24, - -372, - -69, - 94 - ], + "ShimSetting": [585, -7292, -8813, 375, 24, -372, -69, 94], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.88, 0.98, 1.0775, 1.175, 1.2725, 1.37, 1.47, 1.5675, 1.665, 1.7625, 1.86, 1.96, 2.0575, 2.155, 2.2525, 2.35, 2.45, 2.5475, 2.645, 2.7425, 2.84, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_epi.json index 7b677b619..9f25b24b5 100644 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_epi.json +++ b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-05_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99942, - -0.0307991, - 0.0145336, - 0.0340273, - 0.920597, - -0.389028 - ], + "ImageOrientationPatientDICOM": [0.99942, -0.0307991, 0.0145336, 0.0340273, 0.920597, -0.389028], "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-05_ses-010_task-mario3_run-05_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-05_SBRef", "SeriesNumber": 21, - "ShimSetting": [ - 585, - -7292, - -8813, - 375, - 24, - -372, - -69, - 94 - ], + "ShimSetting": [585, -7292, -8813, 375, 24, -372, -69, 94], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.1, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.59, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.08, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.57, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.06, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.55, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.0975, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.5875, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.1, 0.1975, 0.295, 0.3925, 0.49, 0.59, 0.6875, 0.785, 0.8825, 0.98, 1.08, 1.1775, 1.275, 1.3725, 1.47, 1.57, 1.6675, 1.765, 1.8625, 1.96, 2.06, 2.1575, 2.255, 2.3525, 2.45, 2.55, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.0975, 5.195, 5.2925, 5.39, 5.4875, 5.5875, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-06_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-06_epi.json index 246fb59da..0e46f8ab8 100644 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-06_epi.json +++ b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-06_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99942, - -0.0307991, - 0.0145336, - 0.0340273, - 0.920597, - -0.389028 - ], + "ImageOrientationPatientDICOM": [0.99942, -0.0307991, 0.0145336, 0.0340273, 0.920597, -0.389028], "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-05_ses-010_task-mario3_run-06_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-06_SBRef", "SeriesNumber": 24, - "ShimSetting": [ - 585, - -7292, - -8813, - 375, - 24, - -372, - -69, - 94 - ], + "ShimSetting": [585, -7292, -8813, 375, 24, -372, -69, 94], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.1775, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.6675, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.1575, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.6475, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.1375, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.6275, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.1175, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.6075, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.1775, 1.275, 1.3725, 1.47, 1.5675, 1.6675, 1.765, 1.8625, 1.96, 2.0575, 2.1575, 2.255, 2.3525, 2.45, 2.5475, 2.6475, 2.745, 2.8425, 2.94, 3.0375, 3.1375, 3.235, 3.3325, 3.43, 3.5275, 3.6275, 3.725, 3.8225, 3.92, 4.0175, 4.1175, 4.215, 4.3125, 4.41, 4.5075, 4.6075, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-07_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-07_epi.json index 57214b28c..4116e55fe 100644 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-07_epi.json +++ b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-07_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.99942, - -0.0307991, - 0.0145336, - 0.0340273, - 0.920597, - -0.389028 - ], + "ImageOrientationPatientDICOM": [0.99942, -0.0307991, 0.0145336, 0.0340273, 0.920597, -0.389028], "ImageOrientationText": "Tra>Cor(-22.9)>Sag(0.1)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-05_ses-010_task-mario3_run-07_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-07_SBRef", "SeriesNumber": 27, - "ShimSetting": [ - 585, - -7292, - -8813, - 375, - 24, - -372, - -69, - 94 - ], + "ShimSetting": [585, -7292, -8813, 375, 24, -372, -69, 94], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.995, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.4875, 0.5875, 0.685, 0.7825, 0.88, 0.9775, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.995, 5.095, 5.1925, 5.29, 5.3875, 5.485, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-08_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-08_epi.json index 7b12fc354..ae22c8aa1 100644 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-08_epi.json +++ b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-08_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999832, - -0.0126643, - 0.0132834, - 0.0169285, - 0.915955, - -0.400923 - ], + "ImageOrientationPatientDICOM": [0.999832, -0.0126643, 0.0132834, 0.0169285, 0.915955, -0.400923], "ImageOrientationText": "Tra>Cor(-23.6)>Sag(0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-05_ses-010_task-mario3_run-08_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-08_SBRef", "SeriesNumber": 38, - "ShimSetting": [ - 593, - -7311, - -8817, - 363, - 39, - -414, - -59, - 92 - ], + "ShimSetting": [593, -7311, -8817, 363, 39, -414, -59, 92], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.39, - 0.4875, - 0.5875, - 0.685, - 0.7825, - 0.88, - 0.9775, - 1.0775, - 1.175, - 1.2725, - 1.37, - 1.4675, - 1.5675, - 1.665, - 1.7625, - 1.86, - 1.9575, - 2.0575, - 2.155, - 2.2525, - 2.35, - 2.4475, - 2.5475, - 2.645, - 2.7425, - 2.84, - 2.9375, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.4275, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.9175, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.4075, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.8975, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.3875, - 5.485, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.39, 0.4875, 0.5875, 0.685, 0.7825, 0.88, 0.9775, 1.0775, 1.175, 1.2725, 1.37, 1.4675, 1.5675, 1.665, 1.7625, 1.86, 1.9575, 2.0575, 2.155, 2.2525, 2.35, 2.4475, 2.5475, 2.645, 2.7425, 2.84, 2.9375, 3.0375, 3.135, 3.2325, 3.33, 3.4275, 3.5275, 3.625, 3.7225, 3.82, 3.9175, 4.0175, 4.115, 4.2125, 4.31, 4.4075, 4.5075, 4.605, 4.7025, 4.8, 4.8975, 4.9975, 5.095, 5.1925, 5.29, 5.3875, 5.485, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_epi.json index 976dff967..9883a3c84 100644 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_epi.json +++ b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-09_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999832, - -0.0126643, - 0.0132834, - 0.0169285, - 0.915955, - -0.400923 - ], + "ImageOrientationPatientDICOM": [0.999832, -0.0126643, 0.0132834, 0.0169285, 0.915955, -0.400923], "ImageOrientationText": "Tra>Cor(-23.6)>Sag(0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-05_ses-010_task-mario3_run-09_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-09_SBRef", "SeriesNumber": 41, - "ShimSetting": [ - 593, - -7311, - -8817, - 363, - 39, - -414, - -59, - 92 - ], + "ShimSetting": [593, -7311, -8817, 363, 39, -414, -59, 92], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.33, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.82, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.31, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], + "SliceTiming": [0, 0.0975, 0.195, 0.2925, 0.3925, 0.49, 0.5875, 0.685, 0.7825, 0.8825, 0.98, 1.0775, 1.175, 1.2725, 1.3725, 1.47, 1.5675, 1.665, 1.7625, 1.8625, 1.96, 2.0575, 2.155, 2.2525, 2.3525, 2.45, 2.5475, 2.645, 2.7425, 2.8425, 2.94, 3.0375, 3.135, 3.2325, 3.33, 3.43, 3.5275, 3.625, 3.7225, 3.82, 3.92, 4.0175, 4.115, 4.2125, 4.31, 4.41, 4.5075, 4.605, 4.7025, 4.8, 4.9, 4.9975, 5.095, 5.1925, 5.29, 5.39, 5.4875, 5.585, 5.6825, 5.78], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", diff --git a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_epi.json b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_epi.json index 22d1af0de..79bbf15e0 100644 --- a/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_epi.json +++ b/sub-05/ses-010/fmap/sub-05_ses-010_acq-sbref_dir-PA_run-10_epi.json @@ -18,14 +18,7 @@ "FlipAngle": 52, "HeudiconvVersion": "0.5.3.post811+g6206e14", "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.999832, - -0.0126643, - 0.0132834, - 0.0169285, - 0.915955, - -0.400923 - ], + "ImageOrientationPatientDICOM": [0.999832, -0.0126643, 0.0132834, 0.0169285, 0.915955, -0.400923], "ImageOrientationText": "Tra>Cor(-23.6)>Sag(0.4)", "ImageType": [ "ORIGINAL", @@ -33,12 +26,15 @@ "M", "ND", "MOSAIC" - ], +], "ImagingFrequency": 123.259, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", "InstitutionName": "IUGM", "InstitutionalDepartmentName": "Department", + "IntendedFor": [ + "ses-010/func/sub-05_ses-010_task-mario3_run-10_part-mag_bold.nii.gz" +], "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", @@ -67,79 +63,9 @@ "SequenceVariant": "SK\\SS", "SeriesDescription": "func_task-mario3_run-10_SBRef", "SeriesNumber": 44, - "ShimSetting": [ - 593, - -7311, - -8817, - 363, - 39, - -414, - -59, - 92 - ], + "ShimSetting": [593, -7311, -8817, 363, 39, -414, -59, 92], "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.1975, - 0.295, - 0.3925, - 0.49, - 0.5875, - 0.6875, - 0.785, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.275, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.765, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.255, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.745, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.235, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.725, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.215, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.705, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.195, - 5.2925, - 5.39, - 5.4875, - 5.585, - 5.685, - 5.7825 - ], + "SliceTiming": [0, 0.0975, 0.1975, 0.295, 0.3925, 0.49, 0.5875, 0.6875, 0.785, 0.8825, 0.98, 1.0775, 1.175, 1.275, 1.3725, 1.47, 1.5675, 1.665, 1.765, 1.8625, 1.96, 2.0575, 2.155, 2.255, 2.3525, 2.45, 2.5475, 2.645, 2.745, 2.8425, 2.94, 3.0375, 3.135, 3.235, 3.3325, 3.43, 3.5275, 3.625, 3.725, 3.8225, 3.92, 4.0175, 4.115, 4.215, 4.3125, 4.41, 4.5075, 4.605, 4.705, 4.8025, 4.9, 4.9975, 5.095, 5.195, 5.2925, 5.39, 5.4875, 5.585, 5.685, 5.7825], "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 2, "StationName": "MRC35049", From 8c016af5be9622a18fc64794d7754d5ccc7c69e0 Mon Sep 17 00:00:00 2001 From: test Date: Tue, 29 Aug 2023 19:50:52 -0400 Subject: [PATCH 451/463] fix participants.tsv erroneous merges --- participants.tsv | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/participants.tsv b/participants.tsv index 17ce4f7d7..16396d871 100644 --- a/participants.tsv +++ b/participants.tsv @@ -1,2 +1,6 @@ participant_id age sex group sub-01 45 M control +sub-02 51 M control +sub-03 43 F control +sub-05 50 M control +sub-06 41 F control From 613d8febc7035079080dd1890872dd1fea97882d Mon Sep 17 00:00:00 2001 From: test Date: Thu, 31 Aug 2023 14:57:49 -0400 Subject: [PATCH 452/463] [DATALAD] removed content --- .../func/sub-01_ses-008_part-mag_bold.json | 171 ----------------- .../func/sub-01_ses-008_part-mag_bold.nii.gz | 1 - .../func/sub-01_ses-008_part-mag_sbref.json | 149 --------------- .../func/sub-01_ses-008_part-mag_sbref.nii.gz | 1 - .../func/sub-01_ses-008_part-phase_bold.json | 177 ------------------ .../sub-01_ses-008_part-phase_bold.nii.gz | 1 - .../func/sub-01_ses-008_part-phase_sbref.json | 152 --------------- .../sub-01_ses-008_part-phase_sbref.nii.gz | 1 - 8 files changed, 653 deletions(-) delete mode 100644 sub-01/ses-008/func/sub-01_ses-008_part-mag_bold.json delete mode 120000 sub-01/ses-008/func/sub-01_ses-008_part-mag_bold.nii.gz delete mode 100644 sub-01/ses-008/func/sub-01_ses-008_part-mag_sbref.json delete mode 120000 sub-01/ses-008/func/sub-01_ses-008_part-mag_sbref.nii.gz delete mode 100644 sub-01/ses-008/func/sub-01_ses-008_part-phase_bold.json delete mode 120000 sub-01/ses-008/func/sub-01_ses-008_part-phase_bold.nii.gz delete mode 100644 sub-01/ses-008/func/sub-01_ses-008_part-phase_sbref.json delete mode 120000 sub-01/ses-008/func/sub-01_ses-008_part-phase_sbref.nii.gz diff --git a/sub-01/ses-008/func/sub-01_ses-008_part-mag_bold.json b/sub-01/ses-008/func/sub-01_ses-008_part-mag_bold.json deleted file mode 100644 index 51606bc7a..000000000 --- a/sub-01/ses-008/func/sub-01_ses-008_part-mag_bold.json +++ /dev/null @@ -1,171 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:48:9.660000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Unaliased MB4/PE3/LB", - "ImageOrientationPatientDICOM": [0.995016, 0.0929008, 0.0362355, -0.0772611, 0.94797, -0.308843], - "ImageOrientationText": "Tra>Cor(-17.8)>Sag(3.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "M", - "MB", - "ND", - "MOSAIC" -], - "ImagingFrequency": 123.259, - "InPlanePhaseEncodingDirectionDICOM": "COL", - "InstitutionAddress": "Chemin Queen-Mary 4565,Montreal,District,CA,H3W 1W5", - "InstitutionName": "IUGM", - "InstitutionalDepartmentName": "Department", - "MRAcquisitionType": "2D", - "MagneticFieldStrength": 3, - "Manufacturer": "Siemens", - "ManufacturersModelName": "Prisma_fit", - "MatrixCoilMode": "SENSE", - "Modality": "MR", - "MultibandAccelerationFactor": 4, - "PartialFourier": 1, - "PatientPosition": "HFS", - "PercentPhaseFOV": 100, - "PercentSampling": 100, - "PhaseEncodingDirection": "j", - "PhaseEncodingSteps": 104, - "PhaseResolution": 1, - "PixelBandwidth": 2290, - "ProcedureStepDescription": "games^mario3", - "ProtocolName": "func_test", - "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold", - "ReceiveCoilActiveElements": "HC1-7;NC1,2", - "ReceiveCoilName": "HeadNeck_64", - "ReconMatrixPE": 104, - "RepetitionTime": 1.49, - "SAR": 0.0519409, - "ScanOptions": "FS", - "ScanningSequence": "EP", - "SequenceName": "epfid2d1_104", - "SequenceVariant": "SK\\SS", - "SeriesDescription": "func_test", - "SeriesNumber": 7, - "ShimSetting": [635, -7196, -8753, 689, 82, 7, 19, 0], - "SliceThickness": 2, - "SliceTiming": [0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685, 0, 0.7825, 0.0975, 0.8825, 0.195, 0.98, 0.2925, 1.0775, 0.3925, 1.175, 0.49, 1.2725, 0.5875, 1.3725, 0.685], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 259.777, - "WipMemBlock": "2b866f2a-08ca-4c1e-8745-c2aa8dd3ed87||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja", - "dcmmeta_affine": [ - [-1.9900315999984741, -0.15452224016189575, 0.12608401477336884, 110.4366455078125], - [-0.18580162525177002, 1.8959392309188843, -0.6090090870857239, -59.06544876098633], - [0.07247108966112137, 0.617686927318573, 1.9008448123931885, -47.507083892822266], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_reorient_transform": [ - [0.0, -1.0, 0.0, 103.0], - [1.0, 0.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0] -], - "dcmmeta_shape": [104, 104, 60, 9], - "dcmmeta_slice_dim": 2, - "dcmmeta_version": 0.6, - "global": { - "const": { - "AcquisitionMatrix": [104, 0, 0, 104], - "AngioFlag": "N", - "BitsAllocated": 16, - "BitsStored": 16, - "BodyPartExamined": "BRAIN", - "Columns": 832, - "EchoNumbers": 1, - "EchoTime": 37.0, - "EchoTrainLength": 104, - "FlipAngle": 52.0, - "HighBit": 15, - "ImageOrientationPatient": [0.99501579092909, 0.09290081267399, 0.03623554617055, -0.0772611227571, 0.9479696328722, -0.308843478258], - "ImagePositionPatient": [-762.64625454175, -893.96997950852, 214.57324821193], - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "M", - "MB", - "ND", - "MOSAIC" -], - "ImagedNucleus": "1H", - 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"syngo MR E11", - "SpacingBetweenSlices": 2.0000000547342, - "SpecificCharacterSet": "ISO_IR 100", - "StudyID": "1", - "StudyTime": "184432.898000", - "TransmitCoilName": "Body", - "VariableFlipAngleFlag": "N", - "WindowCenterWidthExplanation": "Algo1", - "dBdt": 0.0}, - "slices": {} - }, - "time": { - "samples": { - "AcquisitionNumber": [1, 2, 3, 4, 5, 6, 7, 8, 9], - "AcquisitionTime": ["184809.660000", "184811.150000", "184812.640000", "184814.130000", "184815.620000", "184817.110000", "184818.600000", "184820.090000", "184821.580000"], - "ContentTime": ["184903.269000", "184903.274000", "184903.277000", "184903.280000", "184903.284000", "184903.287000", "184903.291000", "184903.294000", "184903.304000"], - "InstanceCreationTime": ["184903.269000", "184903.274000", "184903.277000", "184903.280000", "184903.284000", "184903.287000", "184903.291000", "184903.294000", "184903.304000"], - "InstanceNumber": [1, 2, 3, 4, 5, 6, 7, 8, 9], - "LargestImagePixelValue": [42344, 42150, 40636, 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-1,149 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:47:59.230000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - "ImageComments": "Single-band reference", - "ImageOrientationPatientDICOM": [ - 0.995016, - 0.0929008, - 0.0362355, - -0.0772611, - 0.94797, - -0.308843 - ], - "ImageOrientationText": "Tra>Cor(-17.8)>Sag(3.6)", - "ImageType": [ - "ORIGINAL", - "PRIMARY", - "M", - "ND", - "MOSAIC" - ], - "ImagingFrequency": 123.259, - 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2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-008/func/sub-01_ses-008_part-mag_sbref.nii.gz b/sub-01/ses-008/func/sub-01_ses-008_part-mag_sbref.nii.gz deleted file mode 120000 index 1c3e3377c..000000000 --- a/sub-01/ses-008/func/sub-01_ses-008_part-mag_sbref.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/Gj/7q/MD5E-s1113795--898662b76381d9412e45bc02d3f4eb68.nii.gz/MD5E-s1113795--898662b76381d9412e45bc02d3f4eb68.nii.gz \ No newline at end of file diff --git a/sub-01/ses-008/func/sub-01_ses-008_part-phase_bold.json b/sub-01/ses-008/func/sub-01_ses-008_part-phase_bold.json deleted file mode 100644 index 118867168..000000000 --- a/sub-01/ses-008/func/sub-01_ses-008_part-phase_bold.json +++ /dev/null @@ -1,177 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:48:9.660000", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of 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"WindowWidth": [18604.0, 18600.0, 18572.0, 18576.0, 18606.0, 18650.0, 18652.0, 18646.0, 18648.0] - }, - "slices": {} - } -} \ No newline at end of file diff --git a/sub-01/ses-008/func/sub-01_ses-008_part-phase_bold.nii.gz b/sub-01/ses-008/func/sub-01_ses-008_part-phase_bold.nii.gz deleted file mode 120000 index 0224d5128..000000000 --- a/sub-01/ses-008/func/sub-01_ses-008_part-phase_bold.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/fw/z5/MD5E-s9928438--2084999bc7789fb6bbbe7896fc4695e9.nii.gz/MD5E-s9928438--2084999bc7789fb6bbbe7896fc4695e9.nii.gz \ No newline at end of file diff --git a/sub-01/ses-008/func/sub-01_ses-008_part-phase_sbref.json b/sub-01/ses-008/func/sub-01_ses-008_part-phase_sbref.json deleted file mode 100644 index 9c88353f6..000000000 --- a/sub-01/ses-008/func/sub-01_ses-008_part-phase_sbref.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "18:47:59.230000", - 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- -7196, - -8753, - 689, - 82, - 7, - 19, - 0 - ], - "SliceThickness": 2, - "SliceTiming": [ - 0, - 0.0975, - 0.195, - 0.2925, - 0.3925, - 0.49, - 0.5875, - 0.685, - 0.7825, - 0.8825, - 0.98, - 1.0775, - 1.175, - 1.2725, - 1.3725, - 1.47, - 1.5675, - 1.665, - 1.7625, - 1.8625, - 1.96, - 2.0575, - 2.155, - 2.2525, - 2.3525, - 2.45, - 2.5475, - 2.645, - 2.7425, - 2.8425, - 2.94, - 3.0375, - 3.135, - 3.2325, - 3.3325, - 3.43, - 3.5275, - 3.625, - 3.7225, - 3.8225, - 3.92, - 4.0175, - 4.115, - 4.2125, - 4.3125, - 4.41, - 4.5075, - 4.605, - 4.7025, - 4.8025, - 4.9, - 4.9975, - 5.095, - 5.1925, - 5.29, - 5.39, - 5.4875, - 5.585, - 5.6825, - 5.78 - ], - "SoftwareVersions": "syngo MR E11", - "SpacingBetweenSlices": 2, - "StationName": "MRC35049", - "TotalReadoutTime": 0.0576811, - "TxRefAmp": 259.777, - "WipMemBlock": "2b866f2a-08ca-4c1e-8745-c2aa8dd3ed87||Sequence: R017 ve11c/master r/75a17815+; Jun 28 2022 16:32:11 by eja" -} \ No newline at end of file diff --git a/sub-01/ses-008/func/sub-01_ses-008_part-phase_sbref.nii.gz b/sub-01/ses-008/func/sub-01_ses-008_part-phase_sbref.nii.gz deleted file mode 120000 index 70976d43a..000000000 --- a/sub-01/ses-008/func/sub-01_ses-008_part-phase_sbref.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/XX/82/MD5E-s1103826--36376e0fdad0cb0e22a410ba88e4a989.nii.gz/MD5E-s1103826--36376e0fdad0cb0e22a410ba88e4a989.nii.gz \ No newline at end of file From 34cd039b715d6318f3b8ef97eeb01eaa78df0bf7 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 8 Dec 2023 09:34:07 -0500 Subject: [PATCH 453/463] fill README --- README | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README b/README index 542b28ae3..dae28d916 100644 --- a/README +++ b/README @@ -1,13 +1,13 @@ -# Courtois-NeuroMod: [xxxx subdataset](https://github.com/courtois-neuromod/xxxxx) +# Courtois-NeuroMod: mario3 subdataset(https://github.com/courtois-neuromod/mario3) The [Courtois project on Neural Modelling (Courtois NeuroMod)](https://www.cneuromod.ca/) aims at training artificial neural networks using extensive experimental data on individual human brain activity and behaviour. -Participants *performed task xxx while functional data being acquired in the MRI scanner* . A extensive description can be found [here](https://docs.cneuromod.ca/en/latest/DATASETS.html#xxxx). +Participants played levels of Mario3 while functional data being acquired in the MRI scanner . A extensive description can be found [here](https://docs.cneuromod.ca/en/latest/DATASETS.html#mario3). This subdataset is organized following the [brain imaging data structure (BIDS)](https://bids.neuroimaging.io/) (including extensions in development) and contains: - [x] [raw neuroimaging data](https://docs.cneuromod.ca/en/latest/MRI.html#functional-sequences) -- [ ] behavioral variables in event files +- [x] behavioral variables in event files - [ ] physiological data - [ ] ECG - [ ] pulse (photoplethysmography) From 854187f91435c5458792b5d1e01ce83ae5973f11 Mon Sep 17 00:00:00 2001 From: test Date: Tue, 12 Dec 2023 16:35:09 -0500 Subject: [PATCH 454/463] [DATALAD] removed content --- ...b-01_ses-020_task-mario3_run-02_events.tsv | 1 - ...-020_task-mario3_run-02_part-mag_bold.json | 172 ----------------- ...20_task-mario3_run-02_part-mag_bold.nii.gz | 1 - ...020_task-mario3_run-02_part-mag_sbref.json | 150 --------------- ...0_task-mario3_run-02_part-mag_sbref.nii.gz | 1 - ...20_task-mario3_run-02_part-phase_bold.json | 178 ------------------ ..._task-mario3_run-02_part-phase_bold.nii.gz | 1 - ...0_task-mario3_run-02_part-phase_sbref.json | 153 --------------- ...task-mario3_run-02_part-phase_sbref.nii.gz | 1 - 9 files changed, 658 deletions(-) delete mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_events.tsv delete mode 100644 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_bold.json delete mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_bold.nii.gz delete mode 100644 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_sbref.json delete mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_sbref.nii.gz delete mode 100644 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_bold.json delete mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_bold.nii.gz delete mode 100644 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_sbref.json delete mode 120000 sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_sbref.nii.gz diff --git a/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_events.tsv b/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_events.tsv deleted file mode 120000 index 1bbdfddb5..000000000 --- a/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_events.tsv +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file diff --git a/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_bold.json b/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_bold.json deleted file mode 100644 index 0d46bd78a..000000000 --- a/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_bold.json +++ /dev/null @@ -1,172 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:55:45.582500", - "BandwidthPerPixelPhaseEncode": 17.17, - 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newline at end of file diff --git a/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_sbref.json b/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_sbref.json deleted file mode 100644 index d1cba77cf..000000000 --- a/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-mag_sbref.json +++ /dev/null @@ -1,150 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:55:35.152500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - "ConsistencyInfo": "N4_VE11C_LATEST_20160120", - "ConversionSoftware": "dcm2niix", - "ConversionSoftwareVersion": "v1.0.20220505", - "DerivedVendorReportedEchoSpacing": 0.000560011, - "DeviceSerialNumber": "167006", - "DwellTime": 2.1e-06, - "EchoTime": 0.037, - "EchoTrainLength": 104, - "EffectiveEchoSpacing": 0.000560011, - "FlipAngle": 52, - "HeudiconvVersion": "0.5.3.post811+g6206e14", - 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b/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_bold.nii.gz deleted file mode 120000 index 416fdf270..000000000 --- a/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_bold.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/76/jK/MD5E-s26476524--4a82ee2f01349ec09d63a9d207844791.nii.gz/MD5E-s26476524--4a82ee2f01349ec09d63a9d207844791.nii.gz \ No newline at end of file diff --git a/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_sbref.json b/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_sbref.json deleted file mode 100644 index f275d1879..000000000 --- a/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_sbref.json +++ /dev/null @@ -1,153 +0,0 @@ -{ - "AcquisitionMatrixPE": 104, - "AcquisitionNumber": 1, - "AcquisitionTime": "11:55:35.152500", - "BandwidthPerPixelPhaseEncode": 17.17, - "BaseResolution": 104, - "BodyPartExamined": "BRAIN", - "CoilCombinationMethod": "Sum of Squares", - 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b/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_sbref.nii.gz deleted file mode 120000 index 255f8fd1f..000000000 --- a/sub-01/ses-020/func/sub-01_ses-020_task-mario3_run-02_part-phase_sbref.nii.gz +++ /dev/null @@ -1 +0,0 @@ -../../../.git/annex/objects/8F/z7/MD5E-s1103842--6cff3d1ff62ef85562aeb9cbceb610f3.nii.gz/MD5E-s1103842--6cff3d1ff62ef85562aeb9cbceb610f3.nii.gz \ No newline at end of file From 7a11dfdbeadf9bf72a619964519ed90af8b44233 Mon Sep 17 00:00:00 2001 From: test Date: Wed, 13 Dec 2023 11:51:50 -0500 Subject: [PATCH 455/463] import all events and bk2 files --- .../ses-001/func/sub-01_ses-001_task-mario3_run-01_events.tsv | 2 +- .../ses-001/func/sub-01_ses-001_task-mario3_run-02_events.tsv | 2 +- .../gamelogs/sub-01_ses-001_task-mario3_level-w1l1_rep-000.bk2 | 1 + .../gamelogs/sub-01_ses-001_task-mario3_level-w1l2_rep-000.bk2 | 1 + .../gamelogs/sub-01_ses-001_task-mario3_level-w1l2_rep-001.bk2 | 1 + 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b/sub-01/ses-003/gamelogs/sub-01_ses-003_task-mario3_level-w5lTower_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/55/zX/MD5E-s2694--cdeb1b9c5890c4b617c82df6dcca1d6b.bk2/MD5E-s2694--cdeb1b9c5890c4b617c82df6dcca1d6b.bk2 \ No newline at end of file diff --git a/sub-01/ses-003/gamelogs/sub-01_ses-003_task-mario3_level-w5lTower_rep-001.bk2 b/sub-01/ses-003/gamelogs/sub-01_ses-003_task-mario3_level-w5lTower_rep-001.bk2 new file mode 120000 index 000000000..d2edf2748 --- /dev/null +++ b/sub-01/ses-003/gamelogs/sub-01_ses-003_task-mario3_level-w5lTower_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/9p/kv/MD5E-s3082--472893b05d513d8eca8f32a50e7e3c7d.bk2/MD5E-s3082--472893b05d513d8eca8f32a50e7e3c7d.bk2 \ No newline at end of file diff --git a/sub-01/ses-003/gamelogs/sub-01_ses-003_task-mario3_level-w5lTower_rep-002.bk2 b/sub-01/ses-003/gamelogs/sub-01_ses-003_task-mario3_level-w5lTower_rep-002.bk2 new file mode 120000 index 000000000..d2d53010d --- /dev/null +++ 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b/sub-01/ses-008/gamelogs/sub-01_ses-008_task-mario3_level-w7l8_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/xX/JQ/MD5E-s3290--f4958fedf42f814156e91b5ec3646a47.bk2/MD5E-s3290--f4958fedf42f814156e91b5ec3646a47.bk2 \ No newline at end of file diff --git a/sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_events.tsv b/sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_events.tsv index 1bbdfddb5..cf8fd11aa 120000 --- a/sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_events.tsv +++ b/sub-01/ses-009/func/sub-01_ses-009_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/FK/WP/MD5E-s2279--6c94f24b0d8641da097a0e88a0d271af.tsv/MD5E-s2279--6c94f24b0d8641da097a0e88a0d271af.tsv \ No newline at end of file diff --git a/sub-01/ses-009/gamelogs/sub-01_ses-009_task-mario3_level-w7l9_rep-000.bk2 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a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-03_events.tsv +++ b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-03_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/7J/WP/MD5E-s5494--405ef8ffaae827f5bdc34514ef936990.tsv/MD5E-s5494--405ef8ffaae827f5bdc34514ef936990.tsv \ No newline at end of file diff --git a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-04_events.tsv b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-04_events.tsv index 1bbdfddb5..cbac54920 120000 --- a/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-04_events.tsv +++ b/sub-01/ses-011/func/sub-01_ses-011_task-mario3_run-04_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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--- /dev/null +++ b/sub-01/ses-021/gamelogs/sub-01_ses-021_task-mario3_level-w7lPiranhaPlant2_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/V7/XX/MD5E-s2515--aca2cd64da112140a64360369e95fefc.bk2/MD5E-s2515--aca2cd64da112140a64360369e95fefc.bk2 \ No newline at end of file diff --git a/sub-01/ses-021/gamelogs/sub-01_ses-021_task-mario3_level-w7lPiranhaPlant2_rep-001.bk2 b/sub-01/ses-021/gamelogs/sub-01_ses-021_task-mario3_level-w7lPiranhaPlant2_rep-001.bk2 new file mode 120000 index 000000000..7e6524395 --- /dev/null +++ b/sub-01/ses-021/gamelogs/sub-01_ses-021_task-mario3_level-w7lPiranhaPlant2_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/J5/PV/MD5E-s2512--a019bd48f024e6298b54cbf03de98a71.bk2/MD5E-s2512--a019bd48f024e6298b54cbf03de98a71.bk2 \ No newline at end of file diff --git a/sub-01/ses-021/gamelogs/sub-01_ses-021_task-mario3_level-w7lPiranhaPlant2_rep-002.bk2 b/sub-01/ses-021/gamelogs/sub-01_ses-021_task-mario3_level-w7lPiranhaPlant2_rep-002.bk2 new file mode 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b/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/Z9/Vv/MD5E-s205425--e556c202429b3c1d0ff6d5318679f32d.tsv/MD5E-s205425--e556c202429b3c1d0ff6d5318679f32d.tsv \ No newline at end of file diff --git a/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-02_events.tsv b/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-02_events.tsv index 1bbdfddb5..ed9ccfe41 120000 --- a/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-02_events.tsv +++ b/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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--- a/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_events.tsv +++ b/sub-01/ses-024/func/sub-01_ses-024_task-mario3_run-04_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/k4/2W/MD5E-s174593--58012ff36c4dd117c1e6850ee819e1cf.tsv/MD5E-s174593--58012ff36c4dd117c1e6850ee819e1cf.tsv \ No newline at end of file diff --git a/sub-01/ses-024/gamelogs/sub-01_ses-024_task-mario3_level-w3l9_rep-000.bk2 b/sub-01/ses-024/gamelogs/sub-01_ses-024_task-mario3_level-w3l9_rep-000.bk2 new file mode 120000 index 000000000..7a4589c05 --- /dev/null +++ b/sub-01/ses-024/gamelogs/sub-01_ses-024_task-mario3_level-w3l9_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/8Q/3w/MD5E-s4653--32dad2e6e855736f046f4f2291dcad29.bk2/MD5E-s4653--32dad2e6e855736f046f4f2291dcad29.bk2 \ No newline at end of file diff --git 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diff --git a/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_events.tsv b/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_events.tsv index 1bbdfddb5..915087069 120000 --- a/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_events.tsv +++ b/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/6f/QV/MD5E-s190185--e70785fbf7a02ad132e4870b4e15c5ef.tsv/MD5E-s190185--e70785fbf7a02ad132e4870b4e15c5ef.tsv \ No newline at end of file diff --git a/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_events.tsv b/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_events.tsv index 1bbdfddb5..67f88522a 120000 --- a/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_events.tsv +++ b/sub-01/ses-025/func/sub-01_ses-025_task-mario3_run-02_events.tsv @@ -1 +1 @@ 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a/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-01_events.tsv +++ b/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/7w/pK/MD5E-s9880--c3744d00f917e8647c6c2c087744c2dd.tsv/MD5E-s9880--c3744d00f917e8647c6c2c087744c2dd.tsv \ No newline at end of file diff --git a/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_events.tsv b/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_events.tsv index 1bbdfddb5..46e2de17d 120000 --- a/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_events.tsv +++ b/sub-02/ses-002/func/sub-02_ses-002_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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a/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-01_events.tsv +++ b/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/pm/QV/MD5E-s11053--c6d4bbf7d55e729416feb8600115bcbe.tsv/MD5E-s11053--c6d4bbf7d55e729416feb8600115bcbe.tsv \ No newline at end of file diff --git a/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_events.tsv b/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_events.tsv index 1bbdfddb5..124cae99c 120000 --- a/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_events.tsv +++ b/sub-02/ses-005/func/sub-02_ses-005_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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diff --git a/sub-02/ses-005/gamelogs/sub-02_ses-005_task-mario3_level-w8lFortress_rep-005.bk2 b/sub-02/ses-005/gamelogs/sub-02_ses-005_task-mario3_level-w8lFortress_rep-005.bk2 new file mode 120000 index 000000000..7f09a2c52 --- /dev/null +++ b/sub-02/ses-005/gamelogs/sub-02_ses-005_task-mario3_level-w8lFortress_rep-005.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/gZ/Kg/MD5E-s2827--8359d842967e3fee58ef2d3912ca0794.bk2/MD5E-s2827--8359d842967e3fee58ef2d3912ca0794.bk2 \ No newline at end of file diff --git a/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_events.tsv b/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_events.tsv index 1bbdfddb5..1052145ef 120000 --- a/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_events.tsv +++ b/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/5w/0j/MD5E-s8545--7331bcacc80de91c911d80bb7500c5f4.tsv/MD5E-s8545--7331bcacc80de91c911d80bb7500c5f4.tsv \ No newline at end of file diff --git a/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_events.tsv b/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_events.tsv index 1bbdfddb5..5c2f67d70 120000 --- a/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_events.tsv +++ b/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/9m/Fp/MD5E-s8346--24e6eec83e85c3f6b29911215a35fde3.tsv/MD5E-s8346--24e6eec83e85c3f6b29911215a35fde3.tsv \ No newline at end of file diff --git a/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_events.tsv b/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_events.tsv index 1bbdfddb5..a4a7ab2db 120000 --- a/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_events.tsv +++ b/sub-02/ses-006/func/sub-02_ses-006_task-mario3_run-03_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/MJ/4k/MD5E-s8925--52a572cedb27a53cd425f1de9a1e2f77.tsv/MD5E-s8925--52a572cedb27a53cd425f1de9a1e2f77.tsv \ No newline at end of file diff --git a/sub-02/ses-006/gamelogs/sub-02_ses-006_task-mario3_level-w1l3_rep-000.bk2 b/sub-02/ses-006/gamelogs/sub-02_ses-006_task-mario3_level-w1l3_rep-000.bk2 new file mode 120000 index 000000000..63e784f0c --- /dev/null +++ b/sub-02/ses-006/gamelogs/sub-02_ses-006_task-mario3_level-w1l3_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/Kx/fF/MD5E-s2586--d23de08f84f454b7d47ecba20c9631aa.bk2/MD5E-s2586--d23de08f84f454b7d47ecba20c9631aa.bk2 \ No newline at end of file diff --git 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b/sub-02/ses-009/gamelogs/sub-02_ses-009_task-mario3_level-w7lFortress2_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/1f/mz/MD5E-s2462--6a1a6edba8e8ba1208364ab80a46caa4.bk2/MD5E-s2462--6a1a6edba8e8ba1208364ab80a46caa4.bk2 \ No newline at end of file diff --git a/sub-02/ses-009/gamelogs/sub-02_ses-009_task-mario3_level-w7lFortress2_rep-001.bk2 b/sub-02/ses-009/gamelogs/sub-02_ses-009_task-mario3_level-w7lFortress2_rep-001.bk2 new file mode 120000 index 000000000..1a1e10493 --- /dev/null +++ b/sub-02/ses-009/gamelogs/sub-02_ses-009_task-mario3_level-w7lFortress2_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/0m/g0/MD5E-s2436--3a0ae1e1ea96a0e86780f84c1339ffe1.bk2/MD5E-s2436--3a0ae1e1ea96a0e86780f84c1339ffe1.bk2 \ No newline at end of file diff --git a/sub-02/ses-009/gamelogs/sub-02_ses-009_task-mario3_level-w7lFortress2_rep-002.bk2 b/sub-02/ses-009/gamelogs/sub-02_ses-009_task-mario3_level-w7lFortress2_rep-002.bk2 new file mode 120000 index 000000000..a9cb96798 --- 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index 000000000..7afd95eb4 --- /dev/null +++ b/sub-02/ses-009/gamelogs/sub-02_ses-009_task-mario3_level-w7lPiranhaPlant2_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/Xk/wx/MD5E-s2511--0df67ef3acf99e34fdd18799bcf844df.bk2/MD5E-s2511--0df67ef3acf99e34fdd18799bcf844df.bk2 \ No newline at end of file diff --git a/sub-02/ses-009/gamelogs/sub-02_ses-009_task-mario3_level-w7lPiranhaPlant2_rep-002.bk2 b/sub-02/ses-009/gamelogs/sub-02_ses-009_task-mario3_level-w7lPiranhaPlant2_rep-002.bk2 new file mode 120000 index 000000000..495ba7f5f --- /dev/null +++ b/sub-02/ses-009/gamelogs/sub-02_ses-009_task-mario3_level-w7lPiranhaPlant2_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/mf/fP/MD5E-s2481--35961683728d74c33bd7ed686008ea2c.bk2/MD5E-s2481--35961683728d74c33bd7ed686008ea2c.bk2 \ No newline at end of file diff --git a/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_events.tsv b/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_events.tsv index 1bbdfddb5..5c00625f6 120000 --- a/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_events.tsv +++ b/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/8j/W4/MD5E-s9040--71eb6c15954ef7b3d901a9f2448e7dc6.tsv/MD5E-s9040--71eb6c15954ef7b3d901a9f2448e7dc6.tsv \ No newline at end of file diff --git a/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_events.tsv b/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_events.tsv index 1bbdfddb5..572261382 120000 --- a/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_events.tsv +++ b/sub-02/ses-010/func/sub-02_ses-010_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_events.tsv b/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_events.tsv index 1bbdfddb5..92efdf477 120000 --- a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_events.tsv +++ b/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/MP/W3/MD5E-s135593--1c08837534a6a58934e4d8e96572236a.tsv/MD5E-s135593--1c08837534a6a58934e4d8e96572236a.tsv \ No newline at end of file diff --git a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_events.tsv b/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_events.tsv index 1bbdfddb5..1ebeefb31 120000 --- a/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_events.tsv +++ b/sub-02/ses-016/func/sub-02_ses-016_task-mario3_run-02_events.tsv @@ -1 +1 @@ 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b/sub-02/ses-016/gamelogs/sub-02_ses-016_task-mario3_level-w7l4_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/Pf/Mx/MD5E-s2727--15d230d56b967d0a97b499b295fe5248.bk2/MD5E-s2727--15d230d56b967d0a97b499b295fe5248.bk2 \ No newline at end of file diff --git a/sub-02/ses-016/gamelogs/sub-02_ses-016_task-mario3_level-w7l5_rep-000.bk2 b/sub-02/ses-016/gamelogs/sub-02_ses-016_task-mario3_level-w7l5_rep-000.bk2 new file mode 120000 index 000000000..f4249fafd --- /dev/null +++ b/sub-02/ses-016/gamelogs/sub-02_ses-016_task-mario3_level-w7l5_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/Zv/x0/MD5E-s2564--1968e077612c02e44f73cc76a3d8e910.bk2/MD5E-s2564--1968e077612c02e44f73cc76a3d8e910.bk2 \ No newline at end of file diff --git a/sub-02/ses-016/gamelogs/sub-02_ses-016_task-mario3_level-w7l5_rep-001.bk2 b/sub-02/ses-016/gamelogs/sub-02_ses-016_task-mario3_level-w7l5_rep-001.bk2 new file mode 120000 index 000000000..3731b2928 --- /dev/null +++ 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b/sub-02/ses-016/gamelogs/sub-02_ses-016_task-mario3_level-w7l7_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/1G/06/MD5E-s2375--59b24fe96ba47ef0d682c3cddb6b59a4.bk2/MD5E-s2375--59b24fe96ba47ef0d682c3cddb6b59a4.bk2 \ No newline at end of file diff --git a/sub-02/ses-016/gamelogs/sub-02_ses-016_task-mario3_level-w7l7_rep-002.bk2 b/sub-02/ses-016/gamelogs/sub-02_ses-016_task-mario3_level-w7l7_rep-002.bk2 new file mode 120000 index 000000000..6c1238552 --- /dev/null +++ b/sub-02/ses-016/gamelogs/sub-02_ses-016_task-mario3_level-w7l7_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/JV/1f/MD5E-s2501--f0a93f3b7dc02734fce8fc16bac0e680.bk2/MD5E-s2501--f0a93f3b7dc02734fce8fc16bac0e680.bk2 \ No newline at end of file diff --git a/sub-02/ses-016/gamelogs/sub-02_ses-016_task-mario3_level-w7lFortress1_rep-000.bk2 b/sub-02/ses-016/gamelogs/sub-02_ses-016_task-mario3_level-w7lFortress1_rep-000.bk2 new file mode 120000 index 000000000..dcaf3f1c2 --- /dev/null +++ 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b/sub-02/ses-016/gamelogs/sub-02_ses-016_task-mario3_level-w7lPiranhaPlant2_rep-002.bk2 new file mode 120000 index 000000000..19dbbf43b --- /dev/null +++ b/sub-02/ses-016/gamelogs/sub-02_ses-016_task-mario3_level-w7lPiranhaPlant2_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/xJ/PK/MD5E-s2504--e198abe1a51aff1ffde179cbda617355.bk2/MD5E-s2504--e198abe1a51aff1ffde179cbda617355.bk2 \ No newline at end of file diff --git a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_events.tsv b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_events.tsv index 1bbdfddb5..cecb12be3 120000 --- a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_events.tsv +++ b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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--- a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-03_events.tsv +++ b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-03_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/JM/08/MD5E-s137954--d9134e2d814b09956eab730c43e28ac8.tsv/MD5E-s137954--d9134e2d814b09956eab730c43e28ac8.tsv \ No newline at end of file diff --git a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_events.tsv b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_events.tsv index 1bbdfddb5..01e76ed85 120000 --- a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_events.tsv +++ b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-04_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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--- a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_events.tsv +++ b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-06_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/xq/xv/MD5E-s180671--0bdfc739943c02a5c51e1b9811f3760a.tsv/MD5E-s180671--0bdfc739943c02a5c51e1b9811f3760a.tsv \ No newline at end of file diff --git a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_events.tsv b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_events.tsv index 1bbdfddb5..3b3a647ec 120000 --- a/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_events.tsv +++ b/sub-02/ses-017/func/sub-02_ses-017_task-mario3_run-07_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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new file mode 120000 index 000000000..f49d5fcda --- /dev/null +++ b/sub-02/ses-017/gamelogs/sub-02_ses-017_task-mario3_level-w8lFortress_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/2X/9x/MD5E-s2717--6e0d1d062e49eb118bc2008a8d5f0544.bk2/MD5E-s2717--6e0d1d062e49eb118bc2008a8d5f0544.bk2 \ No newline at end of file diff --git a/sub-02/ses-017/gamelogs/sub-02_ses-017_task-mario3_level-w8lFortress_rep-001.bk2 b/sub-02/ses-017/gamelogs/sub-02_ses-017_task-mario3_level-w8lFortress_rep-001.bk2 new file mode 120000 index 000000000..5b74b1a2e --- /dev/null +++ b/sub-02/ses-017/gamelogs/sub-02_ses-017_task-mario3_level-w8lFortress_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/KX/mP/MD5E-s2664--7a1d878a8f8455f6feede55c2a4d223b.bk2/MD5E-s2664--7a1d878a8f8455f6feede55c2a4d223b.bk2 \ No newline at end of file diff --git a/sub-02/ses-017/gamelogs/sub-02_ses-017_task-mario3_level-w8lFortress_rep-002.bk2 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+../../../.git/annex/objects/KZ/V4/MD5E-s204600--4eb9d7e2baa7cc0344c29a1e05b8e304.tsv/MD5E-s204600--4eb9d7e2baa7cc0344c29a1e05b8e304.tsv \ No newline at end of file diff --git a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_events.tsv b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_events.tsv index 1bbdfddb5..1150d3211 120000 --- a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_events.tsv +++ b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/Vv/kv/MD5E-s163232--650dd3fa3b6b11c204caa31c1082fa4f.tsv/MD5E-s163232--650dd3fa3b6b11c204caa31c1082fa4f.tsv \ No newline at end of file diff --git a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_events.tsv b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_events.tsv index 1bbdfddb5..fe41a6ece 120000 --- a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_events.tsv +++ b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-03_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/P6/5w/MD5E-s163409--f0d1e397210184469b34fae244012a27.tsv/MD5E-s163409--f0d1e397210184469b34fae244012a27.tsv \ No newline at end of file diff --git a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_events.tsv b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_events.tsv index 1bbdfddb5..cc18a320d 120000 --- a/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_events.tsv +++ b/sub-02/ses-018/func/sub-02_ses-018_task-mario3_run-04_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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+../../../.git/annex/objects/2x/qK/MD5E-s370605--c37a1903192924743509b9d4235e18ac.tsv/MD5E-s370605--c37a1903192924743509b9d4235e18ac.tsv \ No newline at end of file diff --git a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-02_events.tsv b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-02_events.tsv index 1bbdfddb5..decc11705 120000 --- a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-02_events.tsv +++ b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/J2/5m/MD5E-s154066--ee4f6cca361e0718d9115c2051f7fee6.tsv/MD5E-s154066--ee4f6cca361e0718d9115c2051f7fee6.tsv \ No newline at end of file diff --git a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-03_events.tsv b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-03_events.tsv index 1bbdfddb5..8a2bdd4ff 120000 --- a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-03_events.tsv +++ b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-03_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/zf/Vw/MD5E-s142212--d8bca6b3a35995319dc45f1e73e8da1f.tsv/MD5E-s142212--d8bca6b3a35995319dc45f1e73e8da1f.tsv \ No newline at end of file diff --git a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-04_events.tsv b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-04_events.tsv index 1bbdfddb5..34ece04af 120000 --- a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-04_events.tsv +++ b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-04_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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--- a/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_events.tsv +++ b/sub-02/ses-019/func/sub-02_ses-019_task-mario3_run-06_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/6z/ZV/MD5E-s160647--9d3ce1a3a943eb9a9c1c9139451f5717.tsv/MD5E-s160647--9d3ce1a3a943eb9a9c1c9139451f5717.tsv \ No newline at end of file diff --git a/sub-02/ses-019/gamelogs/sub-02_ses-019_task-mario3_level-w1l1_rep-000.bk2 b/sub-02/ses-019/gamelogs/sub-02_ses-019_task-mario3_level-w1l1_rep-000.bk2 new file mode 120000 index 000000000..dc3b14d5d --- /dev/null +++ b/sub-02/ses-019/gamelogs/sub-02_ses-019_task-mario3_level-w1l1_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/6J/Mz/MD5E-s3351--67925edae5a48b87fa2b515ce7b95cbe.bk2/MD5E-s3351--67925edae5a48b87fa2b515ce7b95cbe.bk2 \ No newline at end of file diff --git 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a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-01_events.tsv b/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-01_events.tsv index 1bbdfddb5..d27cd6822 120000 --- a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-01_events.tsv +++ b/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/fV/fj/MD5E-s7623--1cb740830b1c5b6aee175dbe3e3c71c1.tsv/MD5E-s7623--1cb740830b1c5b6aee175dbe3e3c71c1.tsv \ No newline at end of file diff --git a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-02_events.tsv b/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-02_events.tsv index 1bbdfddb5..8bdf4b0d8 120000 --- a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-02_events.tsv +++ b/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-02_events.tsv @@ -1 +1 @@ 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a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-04_events.tsv b/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-04_events.tsv index 1bbdfddb5..31f6a32a0 120000 --- a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-04_events.tsv +++ b/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-04_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/Vq/JG/MD5E-s8082--3a00a5cce631e87657c6218d18aa4871.tsv/MD5E-s8082--3a00a5cce631e87657c6218d18aa4871.tsv \ No newline at end of file diff --git a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-05_events.tsv b/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-05_events.tsv index 1bbdfddb5..b5331973c 120000 --- a/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-05_events.tsv +++ b/sub-03/ses-001/func/sub-03_ses-001_task-mario3_run-05_events.tsv @@ -1 +1 @@ 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a/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-01_events.tsv +++ b/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/qG/jW/MD5E-s5218--522c57fca83678cb340239bc5ceb6119.tsv/MD5E-s5218--522c57fca83678cb340239bc5ceb6119.tsv \ No newline at end of file diff --git a/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_events.tsv b/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_events.tsv index 1bbdfddb5..b915c00ec 120000 --- a/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_events.tsv +++ b/sub-03/ses-002/func/sub-03_ses-002_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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a/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-01_events.tsv +++ b/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/g6/0j/MD5E-s9616--0dbd4cbdfb871d93ebfadea621c0adcc.tsv/MD5E-s9616--0dbd4cbdfb871d93ebfadea621c0adcc.tsv \ No newline at end of file diff --git a/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-02_events.tsv b/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-02_events.tsv index 1bbdfddb5..f0776f9e0 120000 --- a/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-02_events.tsv +++ b/sub-03/ses-004/func/sub-03_ses-004_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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a/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-01_events.tsv +++ b/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/qZ/mV/MD5E-s178639--08cd92d4e88b044fa39be7d0a92c3abf.tsv/MD5E-s178639--08cd92d4e88b044fa39be7d0a92c3abf.tsv \ No newline at end of file diff --git a/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-02_events.tsv b/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-02_events.tsv index 1bbdfddb5..13d878d7e 120000 --- a/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-02_events.tsv +++ b/sub-03/ses-009/func/sub-03_ses-009_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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b/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/Xf/f7/MD5E-s117319--7a6a0bfbdb6541c54de063b9d4778d3e.tsv/MD5E-s117319--7a6a0bfbdb6541c54de063b9d4778d3e.tsv \ No newline at end of file diff --git a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-02_events.tsv b/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-02_events.tsv index 1bbdfddb5..302ec1354 120000 --- a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-02_events.tsv +++ b/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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--- a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-04_events.tsv +++ b/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-04_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/Mw/jz/MD5E-s128017--d6047e2ec566abfc7af339b985daa34e.tsv/MD5E-s128017--d6047e2ec566abfc7af339b985daa34e.tsv \ No newline at end of file diff --git a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-05_events.tsv b/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-05_events.tsv index 1bbdfddb5..ad713c343 120000 --- a/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-05_events.tsv +++ b/sub-03/ses-014/func/sub-03_ses-014_task-mario3_run-05_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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000000000..51192a6bc --- /dev/null +++ b/sub-03/ses-015/gamelogs/sub-03_ses-015_task-mario3_level-w7lPiranhaPlant2_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/9W/kW/MD5E-s2489--bbd7757898a6492a7e3d7139c87174c7.bk2/MD5E-s2489--bbd7757898a6492a7e3d7139c87174c7.bk2 \ No newline at end of file diff --git a/sub-03/ses-015/gamelogs/sub-03_ses-015_task-mario3_level-w8lFortress_rep-000.bk2 b/sub-03/ses-015/gamelogs/sub-03_ses-015_task-mario3_level-w8lFortress_rep-000.bk2 new file mode 120000 index 000000000..5f5021c81 --- /dev/null +++ b/sub-03/ses-015/gamelogs/sub-03_ses-015_task-mario3_level-w8lFortress_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/pg/m0/MD5E-s2677--ba92fdc0e0d3ccd3a1e929ca6b0de1b0.bk2/MD5E-s2677--ba92fdc0e0d3ccd3a1e929ca6b0de1b0.bk2 \ No newline at end of file diff --git a/sub-03/ses-015/gamelogs/sub-03_ses-015_task-mario3_level-w8lFortress_rep-001.bk2 b/sub-03/ses-015/gamelogs/sub-03_ses-015_task-mario3_level-w8lFortress_rep-001.bk2 new file mode 120000 index 000000000..569f82c8b --- /dev/null +++ b/sub-03/ses-015/gamelogs/sub-03_ses-015_task-mario3_level-w8lFortress_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/pZ/5M/MD5E-s2825--50a7b28ff09c91702fed1039a2bd86a1.bk2/MD5E-s2825--50a7b28ff09c91702fed1039a2bd86a1.bk2 \ No newline at end of file diff --git a/sub-03/ses-015/gamelogs/sub-03_ses-015_task-mario3_level-w8lFortress_rep-002.bk2 b/sub-03/ses-015/gamelogs/sub-03_ses-015_task-mario3_level-w8lFortress_rep-002.bk2 new file mode 120000 index 000000000..1aa84cb8b --- /dev/null +++ b/sub-03/ses-015/gamelogs/sub-03_ses-015_task-mario3_level-w8lFortress_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/vq/wf/MD5E-s2669--50ab5921bb1d0ea2f352e4b590605536.bk2/MD5E-s2669--50ab5921bb1d0ea2f352e4b590605536.bk2 \ No newline at end of file diff --git a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_events.tsv b/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_events.tsv index 1bbdfddb5..277728487 120000 --- a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_events.tsv +++ b/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/kQ/pG/MD5E-s132200--b60d385454f4385cf149262f3ac8ad18.tsv/MD5E-s132200--b60d385454f4385cf149262f3ac8ad18.tsv \ No newline at end of file diff --git a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_events.tsv b/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_events.tsv index 1bbdfddb5..7ccce4f5a 120000 --- a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_events.tsv +++ b/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/4q/Wq/MD5E-s161487--06941da531c1a3b0a943d1aa03840802.tsv/MD5E-s161487--06941da531c1a3b0a943d1aa03840802.tsv \ No newline at end of file diff --git a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_events.tsv b/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_events.tsv index 1bbdfddb5..5426e8b3f 120000 --- a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_events.tsv +++ b/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-03_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/wz/P4/MD5E-s111641--3fe8c1abb899a0b0998195e2a0500073.tsv/MD5E-s111641--3fe8c1abb899a0b0998195e2a0500073.tsv \ No newline at end of file diff --git a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_events.tsv b/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_events.tsv index 1bbdfddb5..a25cf3fba 120000 --- a/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_events.tsv +++ b/sub-03/ses-016/func/sub-03_ses-016_task-mario3_run-04_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/0v/05/MD5E-s120694--e2412b08ffc40f97bd7dfd85df2ba08c.tsv/MD5E-s120694--e2412b08ffc40f97bd7dfd85df2ba08c.tsv \ No newline at end of file diff --git a/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w1l5_rep-000.bk2 b/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w1l5_rep-000.bk2 new file mode 120000 index 000000000..a0773f847 --- /dev/null +++ b/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w1l5_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/Gk/18/MD5E-s2593--105a06259294d8dc673181f404c2a402.bk2/MD5E-s2593--105a06259294d8dc673181f404c2a402.bk2 \ No newline at end of file diff --git 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diff --git a/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w3lFortress2_rep-002.bk2 b/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w3lFortress2_rep-002.bk2 new file mode 120000 index 000000000..668a18875 --- /dev/null +++ b/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w3lFortress2_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/m5/4J/MD5E-s2677--82eb715950cdfec5bb3e3efd7ba7f55e.bk2/MD5E-s2677--82eb715950cdfec5bb3e3efd7ba7f55e.bk2 \ No newline at end of file diff --git a/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w4lAirship_rep-000.bk2 b/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w4lAirship_rep-000.bk2 new file mode 120000 index 000000000..9f8d7f1e5 --- /dev/null +++ b/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w4lAirship_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/pp/Kp/MD5E-s3107--1b6a4d300565bb42073948360c37618e.bk2/MD5E-s3107--1b6a4d300565bb42073948360c37618e.bk2 \ No newline at end of file diff --git a/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w4lAirship_rep-001.bk2 b/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w4lAirship_rep-001.bk2 new file mode 120000 index 000000000..591905c74 --- /dev/null +++ b/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w4lAirship_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/JJ/Vv/MD5E-s3200--bf8656d4aa8e6545c5b72eb336056ca9.bk2/MD5E-s3200--bf8656d4aa8e6545c5b72eb336056ca9.bk2 \ No newline at end of file diff --git a/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w4lAirship_rep-002.bk2 b/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w4lAirship_rep-002.bk2 new file mode 120000 index 000000000..f5aa479cb --- /dev/null +++ b/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w4lAirship_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/5k/QG/MD5E-s2740--2d09edd9f861547b91dd6df1d87b28eb.bk2/MD5E-s2740--2d09edd9f861547b91dd6df1d87b28eb.bk2 \ No newline at end of file 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file diff --git a/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w5lTower_rep-000.bk2 b/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w5lTower_rep-000.bk2 new file mode 120000 index 000000000..fdc0544e9 --- /dev/null +++ b/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w5lTower_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/14/k0/MD5E-s2612--cece7ccf9d7433b4d9443a805c2f4251.bk2/MD5E-s2612--cece7ccf9d7433b4d9443a805c2f4251.bk2 \ No newline at end of file diff --git a/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w5lTower_rep-001.bk2 b/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w5lTower_rep-001.bk2 new file mode 120000 index 000000000..a424ed6b5 --- /dev/null +++ b/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w5lTower_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/Vq/2Q/MD5E-s2611--24d5b57c8b10e5539c94b86b2685e997.bk2/MD5E-s2611--24d5b57c8b10e5539c94b86b2685e997.bk2 \ No newline at end of file diff --git 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a/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w7l6_rep-001.bk2 b/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w7l6_rep-001.bk2 new file mode 120000 index 000000000..da4c9d6bc --- /dev/null +++ b/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w7l6_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/11/0z/MD5E-s2514--6462e58abba704feac4a3a748047461d.bk2/MD5E-s2514--6462e58abba704feac4a3a748047461d.bk2 \ No newline at end of file diff --git a/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w7l6_rep-002.bk2 b/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w7l6_rep-002.bk2 new file mode 120000 index 000000000..c9f354135 --- /dev/null +++ b/sub-03/ses-016/gamelogs/sub-03_ses-016_task-mario3_level-w7l6_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/j6/8q/MD5E-s3107--8f6ff74239fdbcd84d115a210077c295.bk2/MD5E-s3107--8f6ff74239fdbcd84d115a210077c295.bk2 \ No newline at end of file diff --git a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-01_events.tsv b/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-01_events.tsv index 1bbdfddb5..77b08dd74 120000 --- a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-01_events.tsv +++ b/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/7G/V7/MD5E-s235803--bd01180222e1a7383b7635c1ce89d8aa.tsv/MD5E-s235803--bd01180222e1a7383b7635c1ce89d8aa.tsv \ No newline at end of file diff --git a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-02_events.tsv b/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-02_events.tsv index 1bbdfddb5..2dde674f6 120000 --- a/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-02_events.tsv +++ b/sub-03/ses-017/func/sub-03_ses-017_task-mario3_run-02_events.tsv @@ -1 +1 @@ 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file mode 120000 index 000000000..fa196fa37 --- /dev/null +++ b/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w1lAirship_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/5M/3p/MD5E-s2603--c087fb9552cf02493384a34fdcd82e6d.bk2/MD5E-s2603--c087fb9552cf02493384a34fdcd82e6d.bk2 \ No newline at end of file diff --git a/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w1lAirship_rep-002.bk2 b/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w1lAirship_rep-002.bk2 new file mode 120000 index 000000000..ed81dfe19 --- /dev/null +++ b/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w1lAirship_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/XZ/5x/MD5E-s2681--522a0168fa8dd7f0255f152cf12ab851.bk2/MD5E-s2681--522a0168fa8dd7f0255f152cf12ab851.bk2 \ No newline at end of file diff --git a/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w2l1_rep-000.bk2 b/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w2l1_rep-000.bk2 new file mode 120000 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b/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w3l7_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/Xx/VW/MD5E-s2855--5b6492310d3c3915d57fd5b8abd8266b.bk2/MD5E-s2855--5b6492310d3c3915d57fd5b8abd8266b.bk2 \ No newline at end of file diff --git a/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w4l1_rep-000.bk2 b/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w4l1_rep-000.bk2 new file mode 120000 index 000000000..e76b2d0be --- /dev/null +++ b/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w4l1_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/Pq/qV/MD5E-s3115--17a31919acf9720a0f52ba666a352904.bk2/MD5E-s3115--17a31919acf9720a0f52ba666a352904.bk2 \ No newline at end of file diff --git a/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w4l3_rep-000.bk2 b/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w4l3_rep-000.bk2 new file mode 120000 index 000000000..c82ee7643 --- /dev/null +++ b/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w4l3_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/1P/0q/MD5E-s2377--252f95c443808ed2fd3ecacb4367b845.bk2/MD5E-s2377--252f95c443808ed2fd3ecacb4367b845.bk2 \ No newline at end of file diff --git a/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w4l3_rep-001.bk2 b/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w4l3_rep-001.bk2 new file mode 120000 index 000000000..39318e455 --- /dev/null +++ b/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w4l3_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/2W/Xk/MD5E-s2325--4fe7717fc2c2c3acfde684996ced1cd3.bk2/MD5E-s2325--4fe7717fc2c2c3acfde684996ced1cd3.bk2 \ No newline at end of file diff --git a/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w4l3_rep-002.bk2 b/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w4l3_rep-002.bk2 new file mode 120000 index 000000000..0447772de --- /dev/null +++ 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b/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w7lFortress1_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/vj/4z/MD5E-s2647--5046d14e24948cbb0dfd05ade7a57b19.bk2/MD5E-s2647--5046d14e24948cbb0dfd05ade7a57b19.bk2 \ No newline at end of file diff --git a/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w7lFortress1_rep-001.bk2 b/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w7lFortress1_rep-001.bk2 new file mode 120000 index 000000000..b18f3d370 --- /dev/null +++ b/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w7lFortress1_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/91/04/MD5E-s2508--e81145d01de60f6f8752c910a7d556a8.bk2/MD5E-s2508--e81145d01de60f6f8752c910a7d556a8.bk2 \ No newline at end of file diff --git a/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w7lFortress1_rep-002.bk2 b/sub-03/ses-017/gamelogs/sub-03_ses-017_task-mario3_level-w7lFortress1_rep-002.bk2 new file mode 120000 index 000000000..1db2b5c89 --- 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b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/6g/Xq/MD5E-s116415--e6ce1c390ff07169ad9e4226f1ec2f7b.tsv/MD5E-s116415--e6ce1c390ff07169ad9e4226f1ec2f7b.tsv \ No newline at end of file diff --git a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-02_events.tsv b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-02_events.tsv index 1bbdfddb5..01f069baf 120000 --- a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-02_events.tsv +++ b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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--- a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-04_events.tsv +++ b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-04_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/q4/72/MD5E-s209831--5ef8948a3413f10ab32edd7890c50349.tsv/MD5E-s209831--5ef8948a3413f10ab32edd7890c50349.tsv \ No newline at end of file diff --git a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-05_events.tsv b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-05_events.tsv index 1bbdfddb5..86b9cba91 120000 --- a/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-05_events.tsv +++ b/sub-03/ses-018/func/sub-03_ses-018_task-mario3_run-05_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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a/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-01_events.tsv +++ b/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/jg/pz/MD5E-s111391--dece8c899585342df32bbe1d98e2e35c.tsv/MD5E-s111391--dece8c899585342df32bbe1d98e2e35c.tsv \ No newline at end of file diff --git a/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_events.tsv b/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_events.tsv index 1bbdfddb5..008cabcbc 120000 --- a/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_events.tsv +++ b/sub-05/ses-001/func/sub-05_ses-001_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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file +../../../.git/annex/objects/0w/0f/MD5E-s103646--24c26873bb1c6bd6dd49878b2581b6ba.tsv/MD5E-s103646--24c26873bb1c6bd6dd49878b2581b6ba.tsv \ No newline at end of file diff --git a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-02_events.tsv b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-02_events.tsv index 1bbdfddb5..9a499197d 120000 --- a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-02_events.tsv +++ b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/J5/FV/MD5E-s98504--179610aac42475f0784577481d408806.tsv/MD5E-s98504--179610aac42475f0784577481d408806.tsv \ No newline at end of file diff --git a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-03_events.tsv b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-03_events.tsv index 1bbdfddb5..d25f60396 120000 --- a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-03_events.tsv +++ b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-03_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/Qv/6Z/MD5E-s153523--98e0599119c1171b3de5acf66f56b1ae.tsv/MD5E-s153523--98e0599119c1171b3de5acf66f56b1ae.tsv \ No newline at end of file diff --git a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-04_events.tsv b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-04_events.tsv index 1bbdfddb5..56c8acc01 120000 --- a/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-04_events.tsv +++ b/sub-05/ses-002/func/sub-05_ses-002_task-mario3_run-04_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-01_events.tsv +++ b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/g2/qz/MD5E-s127428--8c983025d2141794ed53544828a149d6.tsv/MD5E-s127428--8c983025d2141794ed53544828a149d6.tsv \ No newline at end of file diff --git a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_events.tsv b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_events.tsv index 1bbdfddb5..a440821f5 120000 --- a/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_events.tsv +++ b/sub-05/ses-003/func/sub-05_ses-003_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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--- a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-03_events.tsv +++ b/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-03_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/kp/9w/MD5E-s115060--caf25cc75b6e65f5030dc5526b6e9ba9.tsv/MD5E-s115060--caf25cc75b6e65f5030dc5526b6e9ba9.tsv \ No newline at end of file diff --git a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-04_events.tsv b/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-04_events.tsv index 1bbdfddb5..ce81445bb 120000 --- a/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-04_events.tsv +++ b/sub-05/ses-006/func/sub-05_ses-006_task-mario3_run-04_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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/dev/null +++ b/sub-05/ses-006/gamelogs/sub-05_ses-006_task-mario3_level-w8l2_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/Mg/3Z/MD5E-s3058--6a7cc23826f6ba5689098cec5333ff1a.bk2/MD5E-s3058--6a7cc23826f6ba5689098cec5333ff1a.bk2 \ No newline at end of file diff --git a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-01_events.tsv b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-01_events.tsv index 1bbdfddb5..fc73b7d22 120000 --- a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-01_events.tsv +++ b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/0k/WW/MD5E-s101106--3159df0159368f2b4264206895ff749c.tsv/MD5E-s101106--3159df0159368f2b4264206895ff749c.tsv \ No newline at end of file diff --git a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-02_events.tsv b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-02_events.tsv index 1bbdfddb5..92efcd88f 120000 --- a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-02_events.tsv +++ b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/29/X6/MD5E-s96217--164c8d55ad9e500527b5b5d96b135c8a.tsv/MD5E-s96217--164c8d55ad9e500527b5b5d96b135c8a.tsv \ No newline at end of file diff --git a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-03_events.tsv b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-03_events.tsv index 1bbdfddb5..f75ed085d 120000 --- a/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-03_events.tsv +++ b/sub-05/ses-007/func/sub-05_ses-007_task-mario3_run-03_events.tsv @@ -1 +1 @@ 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index 000000000..5a05b9475 --- /dev/null +++ b/sub-05/ses-008/gamelogs/sub-05_ses-008_task-mario3_level-w7lPiranhaPlant2_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/1j/Xx/MD5E-s2468--3a3b0c240bc23f21dc80190b89041933.bk2/MD5E-s2468--3a3b0c240bc23f21dc80190b89041933.bk2 \ No newline at end of file diff --git a/sub-05/ses-008/gamelogs/sub-05_ses-008_task-mario3_level-w7lPiranhaPlant2_rep-002.bk2 b/sub-05/ses-008/gamelogs/sub-05_ses-008_task-mario3_level-w7lPiranhaPlant2_rep-002.bk2 new file mode 120000 index 000000000..8cf1c9cd9 --- /dev/null +++ b/sub-05/ses-008/gamelogs/sub-05_ses-008_task-mario3_level-w7lPiranhaPlant2_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/4K/Z5/MD5E-s2622--97b5d2726913738d1d8964411b0fb91a.bk2/MD5E-s2622--97b5d2726913738d1d8964411b0fb91a.bk2 \ No newline at end of file diff --git a/sub-05/ses-008/gamelogs/sub-05_ses-008_task-mario3_level-w8l1_rep-000.bk2 b/sub-05/ses-008/gamelogs/sub-05_ses-008_task-mario3_level-w8l1_rep-000.bk2 new file mode 120000 index 000000000..089c399ad --- /dev/null +++ b/sub-05/ses-008/gamelogs/sub-05_ses-008_task-mario3_level-w8l1_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/88/5j/MD5E-s2829--3d20eca15f5ad5b40818107140c2ffa8.bk2/MD5E-s2829--3d20eca15f5ad5b40818107140c2ffa8.bk2 \ No newline at end of file diff --git a/sub-05/ses-008/gamelogs/sub-05_ses-008_task-mario3_level-w8l1_rep-001.bk2 b/sub-05/ses-008/gamelogs/sub-05_ses-008_task-mario3_level-w8l1_rep-001.bk2 new file mode 120000 index 000000000..9d656afa5 --- /dev/null +++ b/sub-05/ses-008/gamelogs/sub-05_ses-008_task-mario3_level-w8l1_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/2g/7F/MD5E-s2797--d62b5ee6d46556661e6aae1f493915fa.bk2/MD5E-s2797--d62b5ee6d46556661e6aae1f493915fa.bk2 \ No newline at end of file diff --git a/sub-05/ses-008/gamelogs/sub-05_ses-008_task-mario3_level-w8l1_rep-002.bk2 b/sub-05/ses-008/gamelogs/sub-05_ses-008_task-mario3_level-w8l1_rep-002.bk2 new file mode 120000 index 000000000..cb3b58e4c --- 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b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-02_events.tsv index 1bbdfddb5..4882ccb53 120000 --- a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-02_events.tsv +++ b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/v8/mm/MD5E-s165778--fcca066e26e7fc7e0f3003c1b185c96d.tsv/MD5E-s165778--fcca066e26e7fc7e0f3003c1b185c96d.tsv \ No newline at end of file diff --git a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-03_events.tsv b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-03_events.tsv index 1bbdfddb5..ec87a6f24 120000 --- a/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-03_events.tsv +++ b/sub-05/ses-009/func/sub-05_ses-009_task-mario3_run-03_events.tsv @@ -1 +1 @@ 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b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7l6_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/ZQ/Jv/MD5E-s2454--f584bfd5c482526801b6dcc606ba9bc2.bk2/MD5E-s2454--f584bfd5c482526801b6dcc606ba9bc2.bk2 \ No newline at end of file diff --git a/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7l6_rep-002.bk2 b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7l6_rep-002.bk2 new file mode 120000 index 000000000..846dc2806 --- /dev/null +++ b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7l6_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/v9/Km/MD5E-s2487--3dd31e18bf2f87e4cd4bcf322c0fd028.bk2/MD5E-s2487--3dd31e18bf2f87e4cd4bcf322c0fd028.bk2 \ No newline at end of file diff --git a/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7l8_rep-000.bk2 b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7l8_rep-000.bk2 new file mode 120000 index 000000000..44f0186e4 --- /dev/null +++ b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7l8_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/q2/fw/MD5E-s3235--c4f6ee1611f902f0a3d493b030da5107.bk2/MD5E-s3235--c4f6ee1611f902f0a3d493b030da5107.bk2 \ No newline at end of file diff --git a/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7l8_rep-001.bk2 b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7l8_rep-001.bk2 new file mode 120000 index 000000000..4cf16c29e --- /dev/null +++ b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7l8_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/F7/f9/MD5E-s3163--8c34432db713788a1c5a400d391902f0.bk2/MD5E-s3163--8c34432db713788a1c5a400d391902f0.bk2 \ No newline at end of file diff --git a/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7l8_rep-002.bk2 b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7l8_rep-002.bk2 new file mode 120000 index 000000000..06f5c868a --- /dev/null +++ b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7l8_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/35/JG/MD5E-s3173--7777afcad7dd2a4de9c52f40d92731a5.bk2/MD5E-s3173--7777afcad7dd2a4de9c52f40d92731a5.bk2 \ No newline at end of file diff --git a/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7l9_rep-000.bk2 b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7l9_rep-000.bk2 new file mode 120000 index 000000000..20dc6908d --- /dev/null +++ b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7l9_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/3Z/VF/MD5E-s3502--32d5902e848f34f97de889aeae3e598a.bk2/MD5E-s3502--32d5902e848f34f97de889aeae3e598a.bk2 \ No newline at end of file diff --git a/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7lFortress1_rep-000.bk2 b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7lFortress1_rep-000.bk2 new file mode 120000 index 000000000..d66fa3131 --- /dev/null +++ b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7lFortress1_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/p2/FM/MD5E-s2337--388ea0c4a51b4d54c8e6cbe36a4cc616.bk2/MD5E-s2337--388ea0c4a51b4d54c8e6cbe36a4cc616.bk2 \ No newline at end of file diff --git a/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7lFortress1_rep-001.bk2 b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7lFortress1_rep-001.bk2 new file mode 120000 index 000000000..24ca38ee6 --- /dev/null +++ b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7lFortress1_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/Qx/kW/MD5E-s2501--04537b71513bc352d4235ab13c848236.bk2/MD5E-s2501--04537b71513bc352d4235ab13c848236.bk2 \ No newline at end of file diff --git a/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7lFortress1_rep-002.bk2 b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7lFortress1_rep-002.bk2 new file mode 120000 index 000000000..aa16093c8 --- 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index 000000000..24f15ed5e --- /dev/null +++ b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7lPiranhaPlant1_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/Vp/XV/MD5E-s2272--1beab509c88c3907d24e9f3c4ca6aa00.bk2/MD5E-s2272--1beab509c88c3907d24e9f3c4ca6aa00.bk2 \ No newline at end of file diff --git a/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7lPiranhaPlant1_rep-002.bk2 b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7lPiranhaPlant1_rep-002.bk2 new file mode 120000 index 000000000..98d2111c9 --- /dev/null +++ b/sub-05/ses-009/gamelogs/sub-05_ses-009_task-mario3_level-w7lPiranhaPlant1_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/2Q/xz/MD5E-s2350--236504f0317b693db1c746372129a7c4.bk2/MD5E-s2350--236504f0317b693db1c746372129a7c4.bk2 \ No newline at end of file diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-01_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-01_events.tsv index 1bbdfddb5..147e8ecf4 120000 --- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-01_events.tsv +++ b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/G1/PP/MD5E-s100951--bcd8a4559bb84e26166bd3d4d9b291a3.tsv/MD5E-s100951--bcd8a4559bb84e26166bd3d4d9b291a3.tsv \ No newline at end of file diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-02_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-02_events.tsv index 1bbdfddb5..6b231fcea 120000 --- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-02_events.tsv +++ b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/9F/0G/MD5E-s120595--e400fe4c9b5b91a7af9637d7fe8bef23.tsv/MD5E-s120595--e400fe4c9b5b91a7af9637d7fe8bef23.tsv \ No newline at end of file diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-03_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-03_events.tsv index 1bbdfddb5..b72e3b1a0 120000 --- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-03_events.tsv +++ b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-03_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/kW/QM/MD5E-s121712--51ca3da036fcbbe8f7922c657662f2d5.tsv/MD5E-s121712--51ca3da036fcbbe8f7922c657662f2d5.tsv \ No newline at end of file diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-04_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-04_events.tsv index 1bbdfddb5..7e6a82ced 120000 --- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-04_events.tsv +++ b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-04_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/m1/q9/MD5E-s126213--a2601c89f2e67cbac10a49d1a467f438.tsv/MD5E-s126213--a2601c89f2e67cbac10a49d1a467f438.tsv \ No newline at end of file diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-05_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-05_events.tsv index 1bbdfddb5..1a31b1d6e 120000 --- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-05_events.tsv +++ b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-05_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/Z0/87/MD5E-s128871--f01aa36e1a04804f754d089a16119b82.tsv/MD5E-s128871--f01aa36e1a04804f754d089a16119b82.tsv \ No newline at end of file diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-06_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-06_events.tsv index 1bbdfddb5..5b49a24d2 120000 --- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-06_events.tsv +++ b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-06_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/8Q/7v/MD5E-s119722--e71cc98f461100eec1a8a2c5f9932159.tsv/MD5E-s119722--e71cc98f461100eec1a8a2c5f9932159.tsv \ No newline at end of file diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-07_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-07_events.tsv index 1bbdfddb5..625445b09 120000 --- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-07_events.tsv +++ b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-07_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/M0/65/MD5E-s141989--cf0a5c4596f4b26ed78abf199b64d95b.tsv/MD5E-s141989--cf0a5c4596f4b26ed78abf199b64d95b.tsv \ No newline at end of file diff --git a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-08_events.tsv b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-08_events.tsv index 1bbdfddb5..8905922a4 120000 --- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-08_events.tsv +++ b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-08_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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--- a/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-10_events.tsv +++ b/sub-05/ses-010/func/sub-05_ses-010_task-mario3_run-10_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/Fz/Kq/MD5E-s128672--59cb642d0ca1d98f202afbc3cb332e8b.tsv/MD5E-s128672--59cb642d0ca1d98f202afbc3cb332e8b.tsv \ No newline at end of file diff --git a/sub-05/ses-010/gamelogs/sub-05_ses-010_task-mario3_level-w1l1_rep-000.bk2 b/sub-05/ses-010/gamelogs/sub-05_ses-010_task-mario3_level-w1l1_rep-000.bk2 new file mode 120000 index 000000000..46a8571e4 --- /dev/null +++ b/sub-05/ses-010/gamelogs/sub-05_ses-010_task-mario3_level-w1l1_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/w9/ZV/MD5E-s3317--acae72e43fbe1738b7b5ae122f37dbe6.bk2/MD5E-s3317--acae72e43fbe1738b7b5ae122f37dbe6.bk2 \ No newline at end of file diff --git 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b/sub-06/ses-014/gamelogs/sub-06_ses-014_task-mario3_level-w7l6_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/gf/vg/MD5E-s2952--aa3434487fc71bd9a3d1cceb08b610ea.bk2/MD5E-s2952--aa3434487fc71bd9a3d1cceb08b610ea.bk2 \ No newline at end of file diff --git a/sub-06/ses-014/gamelogs/sub-06_ses-014_task-mario3_level-w7l6_rep-001.bk2 b/sub-06/ses-014/gamelogs/sub-06_ses-014_task-mario3_level-w7l6_rep-001.bk2 new file mode 120000 index 000000000..83561efdd --- /dev/null +++ b/sub-06/ses-014/gamelogs/sub-06_ses-014_task-mario3_level-w7l6_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/m1/27/MD5E-s3125--c3bf7accf79e8a5af877e8370998faeb.bk2/MD5E-s3125--c3bf7accf79e8a5af877e8370998faeb.bk2 \ No newline at end of file diff --git a/sub-06/ses-014/gamelogs/sub-06_ses-014_task-mario3_level-w7l6_rep-002.bk2 b/sub-06/ses-014/gamelogs/sub-06_ses-014_task-mario3_level-w7l6_rep-002.bk2 new file mode 120000 index 000000000..8ad4980f1 --- /dev/null +++ b/sub-06/ses-014/gamelogs/sub-06_ses-014_task-mario3_level-w7l6_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/0F/p2/MD5E-s3083--45bc78bda8913c1bb3b23323d31d4ac6.bk2/MD5E-s3083--45bc78bda8913c1bb3b23323d31d4ac6.bk2 \ No newline at end of file diff --git a/sub-06/ses-014/gamelogs/sub-06_ses-014_task-mario3_level-w7l9_rep-000.bk2 b/sub-06/ses-014/gamelogs/sub-06_ses-014_task-mario3_level-w7l9_rep-000.bk2 new file mode 120000 index 000000000..380f886b5 --- /dev/null +++ b/sub-06/ses-014/gamelogs/sub-06_ses-014_task-mario3_level-w7l9_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/6x/f0/MD5E-s4369--0443a51975fdeabcdab8be1399560f8c.bk2/MD5E-s4369--0443a51975fdeabcdab8be1399560f8c.bk2 \ No newline at end of file diff --git a/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_events.tsv b/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_events.tsv index 1bbdfddb5..798f9194c 120000 --- a/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_events.tsv +++ b/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-01_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file +../../../.git/annex/objects/50/mf/MD5E-s7956--8f81756ac376764bcba37ab3e7fb82fc.tsv/MD5E-s7956--8f81756ac376764bcba37ab3e7fb82fc.tsv \ No newline at end of file diff --git a/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_events.tsv b/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_events.tsv index 1bbdfddb5..3835ad775 120000 --- a/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_events.tsv +++ b/sub-06/ses-015/func/sub-06_ses-015_task-mario3_run-02_events.tsv @@ -1 +1 @@ -../../../.git/annex/objects/3m/PP/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv/MD5E-s116--539045d97ea63aa9bdaf017861ff7ff0.tsv \ No newline at end of file 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a/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w5l8_rep-004.bk2 b/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w5l8_rep-004.bk2 new file mode 120000 index 000000000..372b3b284 --- /dev/null +++ b/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w5l8_rep-004.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/9J/qV/MD5E-s2845--eead03230a25266f97bafcf3ce962dba.bk2/MD5E-s2845--eead03230a25266f97bafcf3ce962dba.bk2 \ No newline at end of file diff --git a/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w6lAirship_rep-000.bk2 b/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w6lAirship_rep-000.bk2 new file mode 120000 index 000000000..82bff13bb --- /dev/null +++ b/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w6lAirship_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/PM/g8/MD5E-s3310--1ef535270bfe1cd66abcf82b5fc79145.bk2/MD5E-s3310--1ef535270bfe1cd66abcf82b5fc79145.bk2 \ No newline at end of file diff --git a/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w6lAirship_rep-001.bk2 b/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w6lAirship_rep-001.bk2 new file mode 120000 index 000000000..13ba6e025 --- /dev/null +++ b/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w6lAirship_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/jM/xp/MD5E-s2843--4a546de564406095eb1e58c8c19887d8.bk2/MD5E-s2843--4a546de564406095eb1e58c8c19887d8.bk2 \ No newline at end of file diff --git a/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w6lAirship_rep-002.bk2 b/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w6lAirship_rep-002.bk2 new file mode 120000 index 000000000..5e55a6387 --- /dev/null +++ b/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w6lAirship_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/j4/zJ/MD5E-s3123--1a4a91a4734da3f6a73e3bdabd9ee717.bk2/MD5E-s3123--1a4a91a4734da3f6a73e3bdabd9ee717.bk2 \ No newline at end of file diff --git a/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w7lFortress2_rep-000.bk2 b/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w7lFortress2_rep-000.bk2 new file mode 120000 index 000000000..0e27acacf --- /dev/null +++ b/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w7lFortress2_rep-000.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/wW/xK/MD5E-s2482--b9781c3f6fe934bc9f96a9bd73aa0f72.bk2/MD5E-s2482--b9781c3f6fe934bc9f96a9bd73aa0f72.bk2 \ No newline at end of file diff --git a/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w7lFortress2_rep-001.bk2 b/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w7lFortress2_rep-001.bk2 new file mode 120000 index 000000000..03bf2fe19 --- /dev/null +++ b/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w7lFortress2_rep-001.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/Gv/00/MD5E-s2549--0d8776ae3e13cac7c75bf7fc080a55b0.bk2/MD5E-s2549--0d8776ae3e13cac7c75bf7fc080a55b0.bk2 \ No newline at end of file diff --git a/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w7lFortress2_rep-002.bk2 b/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w7lFortress2_rep-002.bk2 new file mode 120000 index 000000000..4566a58c3 --- /dev/null +++ b/sub-06/ses-018/gamelogs/sub-06_ses-018_task-mario3_level-w7lFortress2_rep-002.bk2 @@ -0,0 +1 @@ +../../../.git/annex/objects/MW/X8/MD5E-s2436--5a0ded6647d95f0ffe7cbe857a9d8875.bk2/MD5E-s2436--5a0ded6647d95f0ffe7cbe857a9d8875.bk2 \ No newline at end of file From f6b301787649c5caf65f307192328b0936ec4243 Mon Sep 17 00:00:00 2001 From: test Date: Tue, 16 Jan 2024 14:09:07 -0500 Subject: [PATCH 456/463] fix missing bids_template files --- .gitattributes | 2 -- .github/workflows/deploy.yml | 17 +++++++++++++++++ 2 files changed, 17 insertions(+), 2 deletions(-) create mode 100644 .github/workflows/deploy.yml diff --git a/.gitattributes b/.gitattributes index 4fd4f3f43..ca2fe79c4 100644 --- a/.gitattributes +++ b/.gitattributes @@ -10,5 +10,3 @@ sub-*/**/*_events.tsv annex.largefiles=anything *.bk2 annex.largefiles=anything .bidsignore annex.largefiles=nothing -* annex.backend=MD5E -**/.git* annex.largefiles=nothing diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml new file mode 100644 index 000000000..9ab2b36cd --- /dev/null +++ b/.github/workflows/deploy.yml @@ -0,0 +1,17 @@ +name: Test deploy +on: + push: + branches: [ main, git-annex, tests] + pull_request: + branches: [ main ] + workflow_dispatch: +jobs: + deploy_linux: + uses: courtois-neuromod/actions-template/.github/workflows/deploy.yml@main + with: + name: CNeuromod Bot + email: courtois.neuromod@gmail.com + secrets: + ssh_key: ${{ github.event.repository.private && secrets.CNEUROMOD_BOT_SSH_KEY || secrets.CNEUROMOD_USER_BOT_SSH_KEY }} + s3_access_key: ${{ secrets.CNEUROMOD_BOT_S3_ACCESS_KEY }} + s3_secret_key: ${{ secrets.CNEUROMOD_BOT_S3_SECRET_KEY }} From 3259524d62751f108a12093faa471c8d581e17bd Mon Sep 17 00:00:00 2001 From: test Date: Tue, 16 Jan 2024 14:33:25 -0500 Subject: [PATCH 457/463] [DATALAD] Added subdataset --- .gitmodules | 5 +++++ stimuli | 1 + 2 files changed, 6 insertions(+) create mode 100644 .gitmodules create mode 160000 stimuli diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 000000000..25fa5b626 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,5 @@ +[submodule "stimuli"] + path = stimuli + url = git@github.com:courtois-neuromod/mario3.stimuli.git + datalad-id = caf26616-f8f9-41d8-b9b8-6471a4591395 + datalad-url = git@github.com:courtois-neuromod/mario3.stimuli.git diff --git a/stimuli b/stimuli new file mode 160000 index 000000000..6bebdc567 --- /dev/null +++ b/stimuli @@ -0,0 +1 @@ +Subproject commit 6bebdc567354dea7cb836abf8b847a87e38ea1f9 From 532962bc2b607db24bc2128daaecedab2c865c1c Mon Sep 17 00:00:00 2001 From: test Date: Tue, 16 Jan 2024 15:23:32 -0500 Subject: [PATCH 458/463] add deploy workflows to stimuli dataset --- stimuli | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/stimuli b/stimuli index 6bebdc567..3419fdb3b 160000 --- a/stimuli +++ b/stimuli @@ -1 +1 @@ -Subproject commit 6bebdc567354dea7cb836abf8b847a87e38ea1f9 +Subproject commit 3419fdb3b16d14cb140a135e9ef65724753e9b30 From 934a15f15f09079197869275e6182b48aaa9de6a Mon Sep 17 00:00:00 2001 From: test Date: Wed, 17 Jan 2024 10:01:07 -0500 Subject: [PATCH 459/463] ignore bk2s --- .bidsignore | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.bidsignore b/.bidsignore index e6dbe0018..739ba53f1 100644 --- a/.bidsignore +++ b/.bidsignore @@ -1,3 +1,4 @@ **/anat/*localizer* **/anat/*scout* -**/*__dup* +**/*_dup* +**/gamelogs/* From f48ca9cea33e654081dddf0622c5487bbb7ab5d3 Mon Sep 17 00:00:00 2001 From: test Date: Thu, 18 Jan 2024 11:28:40 -0500 Subject: [PATCH 460/463] cleanup --- .heudiconv | 1 - 1 file changed, 1 deletion(-) delete mode 160000 .heudiconv diff --git a/.heudiconv b/.heudiconv deleted file mode 160000 index e47377336..000000000 --- a/.heudiconv +++ /dev/null @@ -1 +0,0 @@ -Subproject commit e47377336d94717649cf3d5e6214e1a615727913 From bb9d7ddc52765bce82d7fa826532f67f0304edae Mon Sep 17 00:00:00 2001 From: test Date: Wed, 27 Mar 2024 10:56:55 -0400 Subject: [PATCH 461/463] fill ds_desc --- dataset_description.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dataset_description.json b/dataset_description.json index 42c9ffff1..39c7b3980 100644 --- a/dataset_description.json +++ b/dataset_description.json @@ -11,7 +11,7 @@ ], "HowToAcknowledge": "https://docs.cneuromod.ca/en/latest/ACCESS.html#how-to-acknowledge", "License": "https://docs.cneuromod.ca/en/latest/ACCESS.html#data-transfer-agreement-(dta)", - "Name": " sub-dataset of the Courtois-Neuromod project", + "Name": "mario3 sub-dataset of the Courtois-Neuromod project", "ReferencesAndLinks": [ "https://docs.cneuromod.ca/" ] From 8ddd9a850c203d2daec116385266508ebb4551eb Mon Sep 17 00:00:00 2001 From: Basile Date: Fri, 31 May 2024 16:00:19 -0400 Subject: [PATCH 462/463] fix README --- README | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README b/README index dae28d916..f587db42f 100644 --- a/README +++ b/README @@ -1,5 +1,5 @@ -# Courtois-NeuroMod: mario3 subdataset(https://github.com/courtois-neuromod/mario3) +# Courtois-NeuroMod: [mario3 subdataset](https://github.com/courtois-neuromod/mario3) The [Courtois project on Neural Modelling (Courtois NeuroMod)](https://www.cneuromod.ca/) aims at training artificial neural networks using extensive experimental data on individual human brain activity and behaviour. From 75ea21faeb05b273de9b884dac8b0c3633ed3263 Mon Sep 17 00:00:00 2001 From: test Date: Fri, 31 May 2024 16:30:13 -0400 Subject: [PATCH 463/463] use datalad-url as workaround for https submodule access --- .gitmodules | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitmodules b/.gitmodules index 25fa5b626..b5c6f5a7b 100644 --- a/.gitmodules +++ b/.gitmodules @@ -2,4 +2,4 @@ path = stimuli url = git@github.com:courtois-neuromod/mario3.stimuli.git datalad-id = caf26616-f8f9-41d8-b9b8-6471a4591395 - datalad-url = git@github.com:courtois-neuromod/mario3.stimuli.git + datalad-url = https://github.com/courtois-neuromod/mario3.stimuli.git